Plant-specific genetic elements and transfer cassettes for plant transformation

ABSTRACT

The present invention provides nucleic acid molecules and sequences, particularly those identified and obtained from plants, that are useful for transferring and integrating one polynucleotide into another via plant transformation techniques.

CROSS-REFERENCE TO RELATED PATENT APPLICATIONS

This application is a U.S. regular application that claims priority toU.S. provisional application Ser. Nos. 60/607,586, filed on Sep. 8,2004, 60/684,525, filed on May 26, 2005, and 60/698,938, filed on Jul.14, 2005, which are all incorporated herein by reference.

FIELD OF THE INVENTION

Described herein are nucleic acid molecules and sequences, particularlythose identified and obtained from plants, that are useful fortransferring and integrating one polynucleotide into another viabacterial-mediated transformation.

BACKGROUND OF THE INVENTION

Bacterial-mediated transformation via, for example, Agrobacterium orRhizobium, entails the transfer and integration of a polynucleotide froma bacterial plasmid into the genome of a eukaryotic organism. The regionof DNA within the bacterial plasmid that is designated for suchmanipulation is called the transfer DNA (“T-DNA”).

A T-DNA region is delimited by left and right “border” sequences, whichare each about twenty-five nucleotides in length and oriented asimperfect direct repeats of the other. T-DNA transfer is initiated by aninitial single stranded nick at the so-called right border site and isterminated by a subsequent secondary nick at the left border site. It isthe resultant single-stranded linear DNA molecule that is transported,by the activity of other proteins, into the plant cell and ultimatelyintegrated into the plant genome.

After initial cleavage at the right border, virD2 covalently binds tothe 5′-side, and the DNA unwinds towards the left border where a secondcleavage reaction occurs. The released single stranded DNA,traditionally referred to as the “T-strand,” is coated with virE2 andprocessed for transfer via type IV type secretion (Lessl and Lanka,(1994) Cell 77: 321-324, 1994; Zupan and Zambryski, Plant Physiol 107:1041-1047, 1997).

Since border sequences alone do not support a highly effective DNAtransfer, extended border regions, generally comprising about 200 ormore base pairs of Agrobacterium tumor-inducing (Ti) plasmid DNA, areused to transform plant cells. Two non-border sequences that are locatedwithin these extended border regions have been shown to promote DNAtransfer, namely the ‘overdrive’ domain of pTi15955 (van Haaren et al.,Nucleic Acids Res. 15: 8983-8997, 1987) and a DNA region containing atleast five repeats of the ‘enhancer’ domain of pRiA4 (Hansen et al.,Plant Mol. Biol., 20:113-122, 1992).

One issue associated with the use of conventional Agrobacterium borderregions is the infidelity of DNA transfer. For instance, primarycleavage reactions at the right border are often not followed bysecondary cleavage reactions at the left border. This “border skipping”leads to the transfer of T-DNAs that are still connected to the rest ofthe plasmid. Such plasmid backbone transfer is undesirable because thesesequences typically comprise antibiotic resistance genes. Plasmidbackbone transfer can also be a consequence of inadvertent right borderactivity at the left border.

A second issue concerns the use of conventional and poorly characterizedAgrobacterium border regions, which permit only very little optimizationof transfer frequencies. This leads to poor transformation rates, andhigh input costs for the production of large numbers of transformedplants.

Furthermore, the presence of foreign T-DNA sequences in food crops isoften perceived as undesirable, and the application of geneticengineering has therefore been limited to a small number of crops thatare destined for feed, oil, fibers, and processed ingredients. Publicconcerns were addressed through development of an all-native approach tomaking genetically engineered plants, as disclosed by Rommens et al. inWO2003/069980, US-2003-0221213, US-2004-0107455, and WO2005/004585,which are all incorporated herein by reference. Rommens et al. teach theidentification and isolation of genetic elements from plants that can beused for bacterium-mediated plant transformation. Thus, Rommens teachesthat a plant-derived transfer-DNA (“P-DNA”), for instance, can beisolated from a plant genome and used in place of an Agrobacterium T-DNAto genetically engineer plants.

The concept of P-DNA mediated transformation has previously beendemonstrated in potato. A 400-base pair potato P-DNA delineated byregions that share sequence identity with the left border of nopalinestrains and the right border of octopine strains was effectivelytransferred from Agrobacterium to plant cells (Rommens et al., PlantPhysiol 135: 421-431, 2004).

The potato P-DNA was subsequently used to introduce a silencingconstruct for a tuber-specific polyphenol oxidase (PPO) gene intopotato. Resulting intragenic plants displayed tolerance against blackspot bruise sensitivity in impacted tubers.

The present invention provides new plant-specific DNA elements thatreplace bacterial borders, and are particularly useful for all-nativeDNA transformation methods.

The present invention also reveals the organization of the extendedregions that are involved in the initiation of DNA transfer by mediatingprimary DNA cleavage, and describes the sequence requirements andspacing of genetic elements that support high activity of the describedelements. Furthermore, the invention shows how manipulations of regionsthat surround enzyme cleavage sites can enhance the fidelity of DNAtransfer.

SUMMARY OF THE INVENTION

One aspect of the present invention is a DNA sequence, comprising apolynucleotide sequences, designated as a “cleavage sites”, thatcomprise the consensus sequence depicted in SEQ ID NO: 84 and which arenot identical to an Agrobacterium transfer-DNA border sequence, nor to apreviously isolated border or border-like sequence.

In one embodiment, a cleavage site is selected from the group consistingof SEQ ID NOs: 8, 9, 11-13, 15-17, 28-37, 38-51, 85-86, 189, 190,194-196, and 198. In one embodiment, the cleavage site represents asynthetic sequence, and is selected from the group consisting of SEQ IDNOs: 8,9 and 11-13. The present invention contemplates a transformationcassette that comprises two cleavage sites. One of those sites may betermed the “primary cleavage site,” while the other may be a “secondarycleavage site.” See FIG. 4.

In another embodiment, the cleavage site is generated by substituting atleast one nucleotide of a cleavage site or cleavage site-like sequenceselected from the group consisting of SEQ ID NOs: 8, 9, 11-13, 15-17,28-86, 190, and 193-198.

In another embodiment, the cleavage site represents a contiguoussequence of a plant genome, and is selected from the group consisting ofSEQ ID NOs: 15-17, 28-37, 38-50, and 85-86.

In yet another embodiment, the cleavage site is derived from a variantof a sequence selected from the group consisting of SEQ ID NOs: 8, 9,11-13, 15-17, 28-37, 38-51, 85-86, 189, 190, 194-196. That is, a variantof any one of these particular sequences is encompassed by the presentinvention so long as the variant sequence permits cleavage by apertinent transformation enzyme and/or enzyme complex involved inbacterium-mediated transformation. Hence, a variant sequence may shareabout 99%, about 98%, about 97%, about 96%, about 95%, about 94%, about93%, about 92%, about 91%, about 90%, about 89%, about 88%, about 87%,about 86%, about 85%, about 84%, about 83%, about 82%, about 81%, about80%, about 79%, about 78%, about 77%, about 76%, about 75%, about 74%,about 73%, about 72%, about 71%, about 70%, about 69%, about 68%, about67%, about 66%, about 65%, about 64%, about 63%, about 62%, about 61%,about 60%, about 59%, about 58%, about 57%, about 56%, about 55%, about54%, about 53%, about 52%, about 51%, or about 50%, or about less than50% sequence identity with of any one of SEQ ID NOs: 8, 9, 11-13, 15-17,28-37, 38-51, 85-86, 189, 190,194-196, so long as the variant sequencecan still be cleaved according to the present invention.

Another aspect of the present invention is a transfer cassette,comprising such a cleavage site positioned upstream from a desiredpolynucleotide. In one embodiment, the cleavage site in the transfercassette is selected from the group consisting of SEQ ID NOs: 8, 9,11-13, 15-17, 28-37, 38-50, 85-86, 189, 190, and 194-196.

In one embodiment, the transfer cassette comprises two cleavage sitesdefined by a first polynucleotide and a second polynucleotide, wherebythe first polynucleotide may comprise a sequence for an “initialcleavage site” that is positioned upstream from the desiredpolynucleotide. The second polynucleotide may comprise a sequence for a“final cleavage site” that is positioned downstream from the desiredpolynucleotide. The two cleavage sites may be positioned as perfect orimperfect direct repeats.

The transfer cassette may further comprise a nucleotide sequencedownstream from the initial cleavage site, whereby this “DI region” is aDNA sequence that (a) comprises at least about 30 base pairs immediatelydownstream from the initial cleavage site, (b) comprises a sequence thatshares at least 70% sequence identity with the DR domain depicted in SEQID NO: 107, that is positioned within about 60 base pairs from theinitial cleavage site, (c) optionally contains multiple sequences thatare identical or inverse complementary to SEQ ID NO: 115, (d) is notidentical to a region that flanks a T-DNA right border in AgrobacteriumTi or Ri plasmids, and (e) supports cleavage activity. The DI region mayenhance the initial cleavage activity by at least 25% compared to thecorresponding sequence of the Ti or Ri plasmid, which does not comprisethe same DI region.

In one embodiment the DI region may share at least 70% sequence identitywith SEQ ID NO: 22, 108-114.

In one embodiment, the transfer cassette further comprises a nucleotidesequence upstream from the final cleavage site, whereby this “UF region”is a DNA sequence that (a) comprises at least 40 base pairs immediatelyupstream from the final cleavage site, (b) comprises at least 55%adenine or thymine residues (AT-rich), (c) comprises a sequence that hasat least 70% sequence identity to either the UL domain depicted in SEQID NO: 120 or the inverse complement of SEQ ID NO: 120 within a distanceof about 50 base pairs from the final cleavage site, (d) optionallycomprises a putative binding site for integration host factor that hasat least 70% sequence identity to the consensus sequence[A/T]-ATCAANNNNTT-[A/G] (SEQ ID NO: 129) or has at least 70% sequenceidentity to the inverse complement of SEQ ID NO: 129, and that ispositioned within 200 base pairs from the final cleavage site or leftborder, (e) is not identical to a region that flanks a T-DNA border inAgrobacterium Ti or Ri plasmids, and (f) supports initial cleavage siteactivity. In one embodiment, the UF region enables transformationfrequencies that are increased, such as by at least 25%, compared to thecorresponding sequence of a Ti or Ri plasmid.

In one embodiment, the UF region may share at least 70% sequenceidentity to the sequences depicted in SEQ ID NO: 184-186 and 211-214.

In another embodiment, the transfer cassette further comprises both a DIand UF element.

Another aspect of the present invention is a transformation vectorcomprising any one of such transfer cassettes, wherein the region of theplasmid backbone that is “upstream from the initial cleavage” (UIregion) comprises at least a 48-nucleotide sequence that containsadenine-rich trinucleotides interspaced by nucleotides that represent,in at least six cases, a cytosine or thymine (pyrimidine) residue,whereby the most downstream pyrimidine represents either the first baseof the initial cleavage site or the base at position −4 relative to theinitial cleavage site. The UI region is not identical to a region thatflanks a T-DNA border of an Agrobacterium or binary plasmid. The UIregion supports initial cleavage activity and may enable transformationfrequencies that are increased, such as by at least 25%, compared to thecorresponding sequence of a Ti or Ri plasmid.

In one embodiment, the UI region of the transformation vector comprisesa nucleotide sequence that has greater than 70% sequence identity to thesequence depicted in SEQ ID NOs: 199-208.

In another embodiment, the region of the plasmid backbone that isassociated with the final cleavage site (AF region) is a DNA sequencethat (a) comprises at least part of the final cleavage site or leftborder and at about two to 40 base pairs flanking downstream DNA, (b)comprises at least four tightly linked clusters of two or more cytosinebases separated by 1-11 other nucleotides, CCN1-11CCN1-11CCN1-11CC (SEQID NO: 122), (c) is not identical to a region that flanks a T-DNA borderin Agrobacterium Ti or Ri plasmids, and (d) supports initial cleavageactivity. In one embodiment, the AF region enables transformationfrequencies that are, for example, at least 25% compared to thecorresponding sequence of a Ti or Ri plasmid.

In one embodiment, the AF region of the transformation vector comprisesa nucleotide sequence that has greater than 70% sequence identity to thesequence depicted in SEQ ID NOs: 187, 188, and 215-218.

The present invention is not limited to the percentage by which initialor final cleavage activity is enhanced by any particular transformationelement described herein. For instance, any of the transformationelements described herein may enhance the initial or final cleavageactivity by 100% or more than 100%, or about 99%, about 98%, about 97%,about 96%, about 95%, about 94%, about 93%, about 92%, about 91%, about90%, about 89%, about 88%, about 87%, about 86%, about 85%, about 84%,about 83%, about 82%, about 81%, about 80%, about 79%, about 78%, about77%, about 76%, about 75%, about 74%, about 73%, about 72%, about 71%,about 70%, about 69%, about 68%, about 67%, about 66%, about 65%, about64%, about 63%, about 62%, about 61%, about 60%, about 59%, about 58%,about 57%, about 56%, about 55%, about 54%, about 53%, about 52%, about51%, about 50%, about 49%, about 48%, about 47%, about 46%, about 45%,about 44%, about 43%, about 42%, about 41%, about 40%, about 39%, about38%, about 37%, about 36%, about 35%, about 34%, about 33%, about 32%,about 31%, about 30%, about 29%, about 28%, about 27%, about 26%, about25%, about 24%, about 23%, about 22%, about 21%, about 20%, about 15%,or about 5% or at least about 1%, compared to a control that does notcomprise the desired transformation element.

The present invention also contemplates transformation cassettes andplasmids, whereby not every transformation element in the constructenhances cleavage activity. Thus, not every element in a cassettedescribed herein must enhance cleavage activity or transformationefficiency in order for it to be useful.

In another aspect of the present invention, a transformation vector isprovided, which comprises (A) a transfer cassette, which comprises, from5′ to 3′, (i) an initial cleavage site, (ii) a DI region, (iii) a UFregion, and (iv) a final cleavage site, and (B) in the transformationplasmid backbone, at least one of (i) a UI region, and (ii) a AF region.

In one aspect, the relevant sequences for DNA transfer of such atransformation vector are shown in SEQ ID NO: 131 and 132.

In one embodiment, the transformation vector further comprises a desiredpolynucleotide positioned between DI and UF region.

In another embodiment, the transformation vector contains at least oneAgrobacterium border as alternative to a cleavage site.

In one embodiment, a putative cleavage site is identified by screeningDNA databases using programs such as BLASTN or a similar program andsearch motifs such as depicted in SEQ ID NO: 130.

In another embodiment, a putative cleavage site is isolated by applyingPCR-based methods described in the Examples.

In yet another embodiment, a DI region or UF region is identified byscreening DNA databases with programs such as BLASTN (Altschul et al.,Nucleic Acids Res. 25: 3389-3402, 1997) using desired domains asqueries.

In one embodiment, a method of identifying a functionally activecleavage site is provided comprising the steps: (a) identifying aputative cleavage site, (b) annealing two primers in such a way that adouble strand DNA sequence is generated comprising the putative cleavagesite, optionally flanked by the sticky ends of specific restrictionenzyme sites, (c) ligating this DNA fragment with a linearized plasmidthat contains replication origins for both E. coli and Agrobacterium,(d) introducing the new plasmid into Agrobacterium, (e) infectingexplants of a plant that is amenable to Agrobacterium-mediatedtransformation with the resulting Agrobacterium strain, (f) applyingtissue culture methods for transformation, proliferation, and, ifnecessary, regeneration (g) allowing callus and/or shoot formation, (h)counting the average number of calli and/or shoots per explant, andcomparing the resulting frequencies with those of conventional controls,(i) selecting putative cleavage sites that support transformation.

In one embodiment, the putative cleavage site may be found to enhancethe transformation efficiency in comparison to an identical plasmid,which does not contain the putative cleavage site. For instance, aputative cleavage site may enhance the transformation efficiency byabout 100% or more than 100%, or about 99%, about 98%, about 97%, about96%, about 95%, about 94%, about 93%, about 92%, about 91%, about 90%,about 89%, about 88%, about 87%, about 86%, about 85%, about 84%, about83%, about 82%, about 81%, about 80%, about 79%, about 78%, about 77%,about 76%, about 75%, about 74%, about 73%, about 72%, about 71%, about70%, about 69%, about 68%, about 67%, about 66%, about 65%, about 64%,about 63%, about 62%, about 61%, about 60%, about 59%, about 58%, about57%, about 56%, about 55%, about 54%, about 53%, about 52%, about 51%,about 50%, about 49%, about 48%, about 47%, about 46%, about 45%, about44%, about 43%, about 42%, about 41%, about 40%, about 39%, about 38%,about 37%, about 36%, about 35%, about 34%, about 33%, about 32%, about31%, about 30%, about 29%, about 28%, about 27%, about 26%, about 25%,about 24%, about 23%, about 22%, about 21%, about 20%, about 15%, orabout 5% or at least about 1%, compared to a control that does notcomprise the putative cleavage site.

In one embodiment, a method of identifying a functionally active DI orUF region is provided comprising the steps; (a) identifying a putativeDNA region, (b) isolating the region from plant DNA using methods suchas PCR, (c) using this region to replace the functional region of atransformation vector, (d) introducing the modified plasmid intoAgrobacterium, (e) infecting explants of a plant that is amenable toAgrobacterium-mediated transformation with the resulting Agrobacteriumstrain, (f) applying tissue culture methods for transformation andproliferation, (g) allowing callus formation, (h) counting the averagenumber of calli per explant, and comparing the resulting frequencies tothose obtained with a conventional control plasmid that does notcomprise the putative DNA region, and (i) identifying a DNA region thatsupports transformation.

In one embodiment, a putative DNA region may be found to enhance thetransformation efficiency in comparison to an identical plasmid, whichdoes not contain the putative DNA region. For instance, a putative DNAregion may enhance the transformation efficiency by about 100% or morethan 100%, or about 99%, about 98%, about 97%, about 96%, about 95%,about 94%, about 93%, about 92%, about 91%, about 90%, about 89%, about88%, about 87%, about 86%, about 85%, about 84%, about 83%, about 82%,about 81%, about 80%, about 79%, about 78%, about 77%, about 76%, about75%, about 74%, about 73%, about 72%, about 71%, about 70%, about 69%,about 68%, about 67%, about 66%, about 65%, about 64%, about 63%, about62%, about 61%, about 60%, about 59%, about 58%, about 57%, about 56%,about 55%, about 54%, about 53%, about 52%, about 51%, about 50%, about49%, about 48%, about 47%, about 46%, about 45%, about 44%, about 43%,about 42%, about 41%, about 40%, about 39%, about 38%, about 37%, about36%, about 35%, about 34%, about 33%, about 32%, about 31%, about 30%,about 29%, about 28%, about 27%, about 26%, about 25%, about 24%, about23%, about 22%, about 21%, about 20%, about 15%, or about 5% or at leastabout 1%, compared to a control that does not comprise the putative DNAregion.

In one embodiment, the step of identifying the putative DNA region maybe accomplished by hybridization studies, where a random or degeneratenucleic acid probe or oligonucleotide is used to identify sequences froma genome that can be subsequently tested for transformation efficacy.For instance, such a probe may be employed in a Southern blot of genomicDNA isolated from a plant, where the probe is essentially based on oneof the transformation elements described herein, e.g., a UF region ofthe present invention.

Alternatively, a preparation of DNA may be subjected to PCR usingprimers that are specific to a particular transformation elementdescribed herein. On the other hand, the primers may be random primersor degenerate primers based on a desired transformation element, thatare employed in a PCR reaction of DNA. The subsequently amplified PCRproduct(s) can be isolated by standard procedures, e.g., via excising itfrom an electrophoretic gel, and then tested according to the presentinvention for transformation efficacy.

In one embodiment, at least one, if not all, of the nucleotide sequencesof the transfer cassette are endogenous to a plant. That is, in oneembodiment, at least one, if not all, of the nucleotide sequences in thetransfer cassette are native to a plant, or are isolated from the sameplant, the same plant species, or from plants that are sexuallyinterfertile with the plant to be transformed. In one embodiment, theplant is a monocotyledonous plant and selected from the group consistingof wheat, turf grass, maize, rice, oat, wheat, barley, sorghum, orchid,iris, lily, onion, banana, sugarcane, and palm.

In another embodiment, the plant is a dicotyledonous plant and selectedfrom the group consisting of potato, tobacco, tomato, avocado, pepper,sugarbeet, broccoli, cassaya, sweet potato, cotton, poinsettia, legumes,alfalfa, soybean, pea, bean, cucumber, grape, brassica, carrot,strawberry, lettuce, oak, maple, walnut, rose, mint, squash, daisy, andcactus.

Another aspect of the present invention is a method for transforming aplant cell, comprising introducing a transformation vector, whichcomprises any one of the transfer cassettes described herein, into aplant cell.

In one embodiment, the plant cell is located in a plant. In anotherembodiment, the plant is selected from the group consisting of wheat,turf grass, maize, rice, oat, wheat, barley, sorghum, orchid, iris,lily, onion, banana, sugarcane, palm, potato, tobacco, tomato, avocado,pepper, sugarbeet, broccoli, cassaya, sweet potato, cotton, poinsettia,legumes, alfalfa, soybean, carrot, strawberry, lettuce, oak, maple,walnut, rose, mint, squash, daisy, and cactus.

In another embodiment, the transformation plasmid is introduced into theplant cell via a bacterium. In one embodiment, the bacterium is fromAgrobacterium, Rhizobium, or Phyllobacterium. In a further embodiment,the bacterium is selected from the group consisting of Agrobacteriumtumefaciens, Rhizobium trifolii, Rhizobium leguminosarum,Phyllobacterium myrsinacearum, SinoRhizobium meliloti, and MesoRhizobiumloti.

In a preferred embodiment, at least one, if not all, of the nucleotidesequences in the transfer cassette are isolated from the same plant, thesame plant species, or plants that are sexually interfertile. In oneembodiment all of the nucleotide sequences are isolated from the sameplant, the same plant species, or from plants that are sexuallyinterfertile.

In one embodiment, a cassette is provided, which comprises (1) a firstpolynucleotide, comprising a sequence that is (i) nicked when exposed toan enzyme involved in bacterial-mediated plant transformation and (ii)not identical to a bacterial border sequence; (2) a secondpolynucleotide, which may be (i) an imperfect or perfect repeat of thefirst polynucleotide, or (ii) a bacterial T-DNA border; (3) a desiredpolynucleotide; and (4) at least one of (a) UI region, (b) DI region,(c) UF region, and (d) AF region.

In one embodiment, the first polynucleotide comprises a sequence that isnative to a plant genome. In another embodiment, the firstpolynucleotide consists essentially of a sequence that is native to aplant genome.

In a preferred embodiment, the first polynucleotide is targeted by a virgene-encoded protein. In one embodiment, the vir gene-encoded protein isVirD2.

In another embodiment, the first polynucleotide conforms to theconsensus sequence depicted in SEQ ID NO: 84. In a preferred embodiment,the first polynucleotide comprises a sequence depicted in any one of thegroup consisting of SEQ ID NOs: 8, 9, 11-13, 15-17, 28-37, 38-51, 85-86,189, 190, 194-196, and 198.

In another embodiment, the first polynucleotide comprises a sequencewith at least 70% sequence identity to the sequence of any one of SEQ IDNO: 28, 85, or 86. In a further embodiment, the first polynucleotidecomprises a sequence that shares at least 70% sequence identity with asequence depicted in any one of SEQ ID NOs: 28-30.

In one embodiment, the first polynucleotide comprises a sequence thatshares at least 70% sequence identity with the sequence depicted in SEQID NO: 32.

In one embodiment, the first polynucleotide comprises a sequence thatshares at least 70% sequence identity with the sequence depicted in SEQID NO: 33.

In one embodiment, the first polynucleotide comprises a sequence thatshares at least 70% sequence identity with the sequence depicted in anyone of SEQ ID NOs: 34-36.

In one embodiment, the first polynucleotide comprises a sequence thatshares at least 70% sequence identity with the sequence depicted in SEQID NO: 37.

In one embodiment, the first polynucleotide comprises a sequence thatshares at least 70% sequence identity with the sequence depicted in anyone of SEQ ID NOs: 195-196.

In one embodiment, the first polynucleotide comprises a sequence thatshares at least 70% sequence identity with the sequence depicted in anyone of SEQ ID NOs: 51 and 194.

In one embodiment, the first polynucleotide comprises a sequence thatshares at least 70% sequence identity with the sequence depicted in anyone of SEQ ID NOs: 189-190.

In one embodiment, the first polynucleotide comprises 1, 2, 3, 4, 5, 6,7, 8, 9, or 10 or more nucleotides that are different in comparison toan Agrobacterium T-DNA border sequence.

In one embodiment, the first polynucleotide is greater than 70%identical in sequence to an Agrobacterium T-DNA border sequence.

In another embodiment, the UI region comprises a sequence that shares atleast 70% sequence identity with at least one of SEQ ID NOs: 199-208.

In another embodiment, the DI region element comprises a sequence thatthat shares at least 70% sequence identity with at least one of SEQ IDNOs: 22, 108-114.

In another embodiment, the UF region element comprises a sequence thatthat shares at least 70% sequence identity with at least part of atleast one of SEQ ID NOs: 184-186 and 211-214. In another embodiment, theAF region comprises a sequence that shares at least 70% sequenceidentity with at least one of SEQ ID NOs: 187, 188, or 215-218.

The present invention encompasses variant sequences of thetransformation elements described herein and is not limited to thepercentage sequence identity that any particular transformation elementmay share with any particular sequence described herein. Thus, thepresent invention encompasses sequences for any of the transformationelements described herein, e.g., a UI region, DI region, UF region, orAF region, that shares about 99%, about 98%, about 97%, about 96%, about95%, about 94%, about 93%, about 92%, about 91%, about 90%, about 89%,about 88%, about 87%, about 86%, about 85%, about 84%, about 83%, about82%, about 81%, about 80%, about 79%, about 78%, about 77%, about 76%,about 75%, about 74%, about 73%, about 72%, about 71%, about 70%, about69%, about 68%, about 67%, about 66%, about 65%, about 64%, about 63%,about 62%, about 61%, about 60%, about 59%, about 58%, about 57%, about56%, about 55%, about 54%, about 53%, about 52%, about 51%, about 50%,about 49%, about 48%, about 47%, about 46%, about 45%, about 44%, about43%, about 42%, about 41%, about 40%, about 39%, about 38%, about 37%,about 36%, about 35%, about 34%, about 33%, about 32%, about 31%, about30%, about 29%, about 28%, about 27%, about 26%, about 25%, about 24%,about 23%, about 22%, about 21%, about 20%, about 15%, or about 5% or atleast about 1% sequence identity with a corresponding sequenceidentified herein.

Another aspect of the present invention contemplates transformationelements such as a UI region, DI region, UF region, or AF region, thatdoes not comprise a nucleotide sequence that is identical to acorresponding region from a bacterium plasmid, such as from atumor-inducing plasmid from Agrobacterium or Rhizobium.

In another embodiment, the AF region element comprises at least 70%sequence identity with at least part of at least one of SEQ ID NO: 187,188, and 215-218.

In another embodiment, the desired polynucleotide is positioned betweenthe first and second polynucleotides, and wherein the desiredpolynucleotide is located downstream from a first polynucleotidecleavage site that functions in initial cleavage.

In a preferred embodiment, the cassette comprises a UI region positionedupstream from the first polynucleotide cleavage site and a AF regionthat is downstream from the second polynucleotide cleavage site.

In one particular embodiment, the portion of the cassette that comprisesthe UI and DI regions comprise the sequence depicted in SEQ ID NO: 131.In one embodiment, the portion of the cassette that comprises the UF andAF regions comprises the sequence depicted in SEQ ID NO: 132.

In one preferred embodiment, all of the DNA sequences between the firstand second polynucleotides are plant DNA. In this regard, the plant DNAis endogenous to (1) a monocotyledonous plant selected from the groupconsisting of wheat, turf grass, maize, rice, oat, wheat, barley,sorghum, orchid, iris, lily, onion, banana, sugarcane, and palm; or (2)a dicotyledonous plant selected from the group consisting of potato,tobacco, tomato, avocado, pepper, sugarbeet, broccoli, cassaya, sweetpotato, cotton, poinsettia, legumes, alfalfa, soybean, carrot,strawberry, lettuce, oak, maple, walnut, rose, mint, squash, daisy, andcactus, cucumber, melon, canola, apple, or pine.

In another embodiment, the cassette further comprises at least one of(1) an overdrive element, comprising a sequence that is at least 70%identical in sequence to SEQ ID NO: 88; (2) a pyrimidine-rich element,comprising a sequence that shares at least 70% sequence identity withany one of SEQ ID NOs: 199-208 but which is not identical to anAgrobacterium plasmid sequence that flanks a right border; (2) anAT-rich element, comprising a sequence that shares at least 70% sequenceidentity to at least part of any one of SEQ ID NOs: 184-186 and 211-214;and (4) a cytosine cluster, comprising a sequence at least 70% sequenceidentity to at least part of any one of SEQ ID NOs: 187-188 and 215-218.

The present invention also provides a plant transformation cassette,which comprises at least one of (1) a polynucleotide comprising asequence depicted in any one of the group consisting of SEQ ID NOs: 8,9, 11-13, 15-17, 28-50, 85, 86, and 190 or any other cleavage sitesequence disclosed herein, wherein the 3′-end of the polynucleotideabuts a cytosine cluster, e.g., wherein the sequence comprising the3′-end of the polynucleotide and DNA downstream thereof, comprises thesequence depicted in SEQ ID NO: 122; and (2) a polynucleotide comprisinga sequence depicted in any one of the group consisting of SEQ ID NOs: 8,9, 11-13, 15-17, 28-50, 85, and 86 or any other cleavage site disclosedherein, wherein the 5′-end of the polynucleotide abuts a UI region.

In one embodiment, the cytosine cluster comprises a sequence that sharesat least 70% sequence identity with any one of the sequences in SEQ IDNOs: 187-188.

In another embodiment, the UI region comprises a sequence that shares atleast 70% sequence identity with any one of the sequences in SEQ ID NOs:199, 209, and 210.

In another embodiment, a plant transformation cassette is provided,which comprises at least one of (1) a polynucleotide comprising asequence depicted in any one of the group consisting of SEQ ID NOs: 8,9, 11-13, 15-17, 28-50, 85, 86, and 190, wherein the 3′-end of thepolynucleotide abuts a cytosine cluster; (2) a polynucleotide comprising(i) a sequence depicted in any one of the group consisting of SEQ IDNOs: 8, 9, 11-13, 15-17, 28-37, 38-51, 85-86, 189, 194-196, and 198, and(ii) a DNA sequence positioned downstream of the sequence of (i),wherein the sequences of (i) and (ii) together comprise a cytosinecluster; and (3) a polynucleotide comprising a sequence depicted in anyone of the group consisting of SEQ ID NOs: 8, 9, 11-13, 15-17, 28-37,38-51, 85-86, 189, 194-196, and 198, wherein the 5′-end of thepolynucleotide abuts a pyrimidine-rich element. In one embodiment, thecytosine cluster comprises a sequence that shares at least 70% sequenceidentity with any one of the sequences in SEQ ID NOs: 187-188. Inanother embodiment, the pyrimidine-rich element comprises a sequencethat shares at least 70% sequence identity with any one of the sequencesin SEQ ID NOs: 21 and 199-208.

Another aspect of the present invention is a method for transforming aplant cell, which comprises introducing any one of the cassettes orplant transformation cassettes described herein into a plant cell. Sucha cassette may be positioned within a plant transformation plasmid, suchas a Ti- or Ri-plasmid.

Thus, in one particular embodiment, a cassette of the present inventionis placed in a vector, which is derived from a tumor-inducing cassettefrom an Agrobacterium, Rhizobium, or Phyllobacterium bacterium, andwhich is suitable for plant transformation.

In one embodiment, the bacterium is selected from the group consistingof Agrobacterium tumefaciens, Rhizobium trifolii, Rhizobiumleguminosarum, Phyllobacterium myrsinacearum, SinoRhizobium meliloti,and MesoRhizobium loti.

In another embodiment of this method, the vector housing the desiredcassette is maintained in a strain of one of these bacteria and it isthe bacterium strain that is used to infect the plant cell and therebyintroduce the cassette or plant transformation cassette into the plantcell.

In one embodiment, the plant cell is located in either (1) amonocotyledonous plant or explant thereof selected from the groupconsisting of wheat, turf grass, maize, rice, oat, wheat, barley,sorghum, orchid, iris, lily, onion, banana, sugarcane, and palm; or (2)a dicotyledonous plant or explant thereof selected from the groupconsisting of potato, tobacco, tomato, avocado, pepper, sugarbeet,broccoli, cassaya, sweet potato, cotton, poinsettia, legumes, alfalfa,soybean, carrot, strawberry, lettuce, oak, maple, walnut, rose, mint,squash, daisy, and cactus.

In one particular embodiment, a tomato plant is transformed using acassette in which the first polynucleotide in the cassette comprises asequence that shares at least 70% sequence identity with any one of thesequences of SEQ ID NO: 28-30.

In another embodiment, an alfalfa plant is transformed using a cassettein which the first polynucleotide comprises a sequence that shares atleast 70% sequence identity to the sequence depicted in SEQ ID NO: 32.

In another embodiment, a barley plant is transformed using a cassette inwhich the first polynucleotide comprises a sequence that shares at least70% sequence identity to the sequence depicted in SEQ ID NO: 33.

In another embodiment, a rice plant is transformed using a cassette inwhich the first polynucleotide comprises a sequence that shares at least70% sequence identity to the sequence depicted in SEQ ID NOs: 34-36.

In another embodiment, a wheat plant is transformed using a cassette inwhich the first polynucleotide comprises a sequence that shares at least70% sequence identity to the sequence depicted in SEQ ID NO: 37.

In another embodiment, a soybean plant is transformed using a cassettein which the first polynucleotide comprises a sequence that shares atleast 70% sequence identity to the sequence depicted in any one of SEQID NOs: 195-196.

In another embodiment, a maize plant is transformed using a cassette inwhich the first polynucleotide comprises a sequence that shares at least70% sequence identity to the sequence depicted in any one SEQ ID NOs: 51and 194.

In another embodiment, a Brassica plant is transformed using a cassettein which the first polynucleotide comprises a sequence that shares atleast 70% sequence identity to one of the sequences depicted in SEQ IDNOs: 189 or 198. In one embodiment, the plant to be transformed is aBrassica plant.

The present invention does not limit which polynucleotide sequence canbe used to transform a particular plant. Thus, a first polynucleotidethat comprises a sequence that shares at least 70% sequence identity tothe sequence depicted in any one of SEQ ID NOs: 51 and 194, can be usedto transform a potato plant, instead of maize. Hence, the presentinvention contemplates various permutations of transformation elementsand their usefulness in transforming a variety of plants and organisms.According to the present invention, an animal cell may be transformedusing any of the cassettes or plasmids described herein. Hence, in oneembodiment, an animal cell may be transformed with genetic elements thatare native to the animal and its species, thereby providing an“all-native” approach to transforming animal cells and animals.

In one particular embodiment, the monocotyledonous or dicotyledonousexplant is a seed, germinating seedling, leaf, root, stem, cutting, orbud.

According to these methods, the bacterium that is used to perform theplant transformation can be an Agrobacterium, Rhizobium, orPhyllobacterium bacterium. In one embodiment, the bacterium is selectedfrom the group consisting of Agrobacterium tumefaciens, Rhizobiumtrifolii, Rhizobium leguminosarum, Phyllobacterium myrsinacearum,SinoRhizobium meliloti, and MesoRhizobium loti.

In one embodiment, the bacterial T-DNA border of the cassette describedherein is from Agrobacterium tumefaciens, Rhizobium trifolii, Rhizobiumleguminosarum, Phyllobacterium myrsinacearum, SinoRhizobium meliloti, orMesoRhizobium loti.

Another aspect of the present invention is a cassette, which comprises(1) a first polynucleotide, comprising a sequence that is nicked whenexposed to an enzyme involved in bacterial-mediated plant transformationand; (2) a second polynucleotide that has greater than 70% sequenceidentity to any one of SEQ ID NOs: 133-137. In one embodiment, thecassette further comprises a desired polynucleotide. In anotherembodiment the first polynucleotide is a bacterial T-DNA right bordersequence. In another embodiment, the first polynucleotide is notidentical in sequence to a bacterial T-DNA right border sequence. Thesequence of the first polynucleotide may comprise the sequence depictedin any one of SEQ ID NOs: 8, 9, 11-13, 15-17, 28-50, 85, 86, 189, 190,and 194-196.

In another aspect, a transposase-transposon, plant transformationcassette is provided, which comprises (i) left and right transfer-DNAborder sequences; (ii) a non-autonomous transposable element; and (iii)a transposase gene, wherein the non-autonomous transposable element andthe transposase gene are positioned between the left and right bordersequences.

In one embodiment, the plant transformation cassette comprises at leastone of the border sequences comprising a sequence that is (i) nickedwhen exposed to an enzyme involved in bacterial-mediated planttransformation and (ii) is not identical to a bacterial border sequence.The sequence of the first polynucleotide may comprise the sequencedepicted in any one of SEQ ID NOs: 8, 9, 11-13, 15-17, 28-50, 85, 86,189, 190, and 194-196.

In one embodiment, in this cassette, at least one of the bordersequences is a bacterial T-DNA border. In another embodiment, thecassette further comprises a desired polynucleotide positioned withinthe non-autonomous transposable element.

In one embodiment, the terminal ends of the non-autonomous transposableelement are those from maize transposable element Ac.

In a further embodiment, the desired polynucleotide is positioned atleast 80-200 nucleotides from either terminal end of the non-autonomoustransposable element, such as an Ac element. In one embodiment, oneterminal end of the Ac element comprises the sequence depicted in SEQ IDNO: 139 and wherein the other terminal end of the Ac element comprisesthe sequence depicted in SEQ ID NO: 140. In one embodiment, SEQ ID NO:139 is at the 5′-end of the Ac element, while SEQ ID NO: 140 is at the3′-end of the Ac element.

In a preferred embodiment, the non-autonomous transposable element is anAc, Spm, or Mu transposable element.

In one embodiment, the transposase gene is operably linked to aregulatory elements that can express the transposase gene.

This transposase-transposon cassette may be in a plasmid that is presentin a bacterium strain selected from the group consisting ofAgrobacterium tumefaciens, Rhizobium trifolii, Rhizobium leguminosarum,Phyllobacterium myrsinacearum, SinoRhizobium meliloti, and MesoRhizobiumloti. Hence, one method of the present invention is a method fortransforming a plant with a desired polynucleotide, comprising infectinga plant with such a bacterium strain that contains thetransposase-transposon cassette.

Another aspect of the present invention is a method for transforming aplant, comprising infecting a plant with any one of thetransposon-transposase cassettes of the present invention.

Another aspect of the present invention is a method for transforming aplant, comprising (1) transforming a plant with a transformation plasmidthat is suitable for bacterium-mediated plant transformation, whereinthe plasmid comprises a transfer-DNA that is delineated by (i) left andright transfer-DNA border sequences, and which comprises (ii) anon-autonomous transposable element, which comprises a desiredpolynucleotide, and a (iii) a transposase gene, wherein thenon-autonomous transposable element and the transposase gene arepositioned between the left and right border sequences, and (2)selecting a plant that stably comprises in its genome the non-autonomoustransposable element but not the transfer-DNA.

In one embodiment, at least one of the border sequences of this methodcomprises a sequence that is (i) nicked when exposed to an enzymeinvolved in bacterial-mediated plant transformation and (ii) notidentical to a bacterial border sequence.

In another embodiment, the sequence of at least one of the bordersequences comprises the sequence depicted in any one of SEQ ID NOs: 8,9, 11-13, 15-17, 28-37, 38-51, 85-86, 189, 190, 194-196, and 198.

In another embodiment, the step of selecting a plant comprisespositively selecting for a plant that comprises the non-autonomoustransposable element and counter-selecting against a plant thatcomprises the transfer-DNA. In another embodiment, the non-autonomoustransposable element comprises the terminal ends of any one of an Ac,Spm, or Mu transposable element. In one embodiment, one terminal end ofthe Ac element comprises the sequence depicted in SEQ ID NO: 139 andwherein the other terminal end of the Ac element comprises the sequencedepicted in SEQ ID NO: 140. In another embodiment, the transposase geneis operably linked to regulatory elements that permit expression of thetransposase gene in a plant cell.

In another embodiment, the plasmid that is used to infect the plant ismaintained in a bacterium strain selected from the group consisting ofAgrobacterium tumefaciens, Rhizobium trifolii, Rhizobium leguminosarum,Phyllobacterium myrsinacearum, SinoRhizobium meliloti, and MesoRhizobiumloti. Accordingly, the present invention also encompasses a method fortransforming a plant with a desired polynucleotide, comprising infectinga plant with one of these bacterium strains that contains thetransposon-transposase plasmid.

In another embodiment, a cassette is provided, which comprises (1) afirst polynucleotide, comprising a sequence that is (i) nicked whenexposed to an enzyme involved in bacterial-mediated plant transformationand (ii) not identical to a bacterial border sequence; (2) a secondpolynucleotide, which may be (i) an imperfect or perfect repeat of thefirst polynucleotide, or (ii) a bacterial T-DNA border; and (3) a regioncomprising a virC2 gene, which may be flanked by regulatory sequences.

In one embodiment, the region that comprises the virC2 gene, comprisesthe sequence depicted in SEQ ID NO: 167. In another embodiment, thecassette is in a plasmid suitable for bacterium-mediated transformation.

Another aspect of the present invention is a method for transforming aplant with a desired polynucleotide, comprising infecting the plant witha bacterium strain comprising any plasmid described herein, wherein thebacterium strain selected from the group consisting of Agrobacteriumtumefaciens, Rhizobium trifolii, Rhizobium leguminosarum,Phyllobacterium myrsinacearum, SinoRhizobium meliloti, and MesoRhizobiumloti.

In one embodiment, one or more of the polynucleotides, regions,elements, or domains described herein are not 100% identical innucleotide sequence to a corresponding bacterium sequence. For instance,a polynucleotide comprising a sequence for a cleavage site according tothe present invention, is not 100% identical across its length to anAgrobacterium right border sequence.

A transformation cassette may comprise, therefore, sequences thatfacilitate plant transformation, some, if not all, of which may or maynot be identical to a corresponding bacterium sequence. Alternatively,the transformation cassette may comprise one or more bacterialsequences. Thus, the present invention contemplates various permutationsof nucleic acid molecules that cover transformation cassettes with nobacterial sequences as well as those that do. For instance, aplant-derived cleavage site might be used in conjunction with a leftborder sequence from an Agrobacterium T-DNA.

Another aspect of the present invention, is a method for identifying apolynucleotide sequence that is involved in bacterium-mediated planttransformation, comprising:

-   -   (i) isolating a candidate sequence from a source of genetic        material;    -   (ii) operably replacing one of (a) the first or second        polynucleotide, (b) the UI region, (c) the DI region, (d) the UF        region, or (e) the AF region of the cassette of claim 1, with        the candidate sequence;    -   (iii) infecting a plant with the cassette using        bacterium-mediated transformation; and    -   (iv) determining whether the plant is stably transformed with        the desired polynucleotide, wherein a plant that is transformed        with the desired polynucleotide indicates that the candidate        sequence is involved in bacterium-mediated plant transformation.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Sequence requirements for 25-bp cleavage sites. Mismatches tothe consensus of Agrobacterium Right Borders (CON1) are bold andunderlined. Horizontal bars show transformation frequencies compared tothose supported by the conventional Right Border Rb02 and the syntheticcontrol cleavage site Ct01, and represent the mean of at least threeexperiments. The accession numbers of sequences identified in publicdatabases are shown between parentheses. Sequences that were isolated byemploying PCR/inverse PCR approaches are indicated with asterisks. (A)Agrobacterium Right Borders, indicated as Rb, are derived from plasmidsof A. tumefaciens (Rb01, Rb02), A. rhizogenes (Rb03, Rb04, Rb05, Rb06and Rb07), and A. vitis (Rb04). (B) Synthetic elements are indicatedwith Sy. (C) The sequences of plant-derived cleavage sites or cleavagesite-like sequences are designated with the initials of the species namefollowed by a number. (D) The overall consensus for both functionalRight Borders and cleavage sites is indicated by CON2.

FIG. 2. Sequences flanking right border alternatives. (A) Upstreamsequences display a conserved organization of cytosine/thymine residuesseparated by adenine-rich trinucleotide spacers. The overdrive sequenceof pTi15955 is underlined (dotted). Direct repeats are indicated withgrey arrows. Transformation efficacies are shown between parentheses aspercentages of controls, and represent the mean±SE of three experiments.“+1” indicates the position of the first base of the right border orright border alternative. ND=not determined. (B) Helical stabilityprofile (kcal/mol) across the extended 2-kb St02 region of pSIM551 with60-bp step size and 120-bp window size. (C) Downstream sequencescomprise a DR domain (bold) at a distance of one to 27 nucleotides fromthe border. Plasmids pSIM781, 793, and 843 contain DNA fragments from apotato homolog of AY566555, a potato homolog of AY972080, and an alfalfahomolog of Medicago truncatula AC131026, respectively. Plasmid pSIM582contains Le01 flanked by the same tomato DNA sequence that flanks theelement in its original genomic context. The 5′-GCCC motif isunderlined. Transformation frequencies are shown between parentheses aspercentages of controls, and represent the mean±SE of three experiments.

FIG. 3. DNA sequences flanking left borders and left borderalternatives. Upstream DNA is italicized with UL domain indicated inbold. Left borders and left border alternatives are highlighted in grey.Cytosine clusters are boxed. Frequencies of transgenic plants containingthe designated transfer DNA delineated by borders or border alternatives(‘T’), the transfer DNA still attached to backbone sequences (‘TB’), andbackbone-only (‘B’) are shown on the right and represent the mean±SE ofthree experiments. ND=not determined.

FIG. 4. General organization of extended border regions. Putative sitesfor DnaA and IHF are indicated with open vertical arrows. The primarycleavage and secondary cleavage sites are represented by open boxes. Thecleavage sites could be considered to correspond to transfer-DNA rightand left borders, respectively. The direction in which DNA unwinds isindicated with a dashed horizontal arrow.

FIG. 5. Schematic of a transposon-transposase construct of the presentinvention.

FIG. 6. Plasmid maps: (A) pSIM551, pSIM578, pSIM579, pSIM580, andpSIM581; (B) pSIM843B, pSIM108, pSIM831, pSIM829, pSIM401, and pSIM794;(C) pSIM1026, pSIM1008, pSIM781, pSIM844, and pSIM827. “Ori Ec” denotesan origin of replication from bacteria, including E. coli. “Ori At”denotes an origin of replication from bacteria, including Agrobacteriumtumifaciens.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present invention provides a variety of DNA sequences that arecapable of initiating and facilitating the transfer of onepolynucleotide into another via standard plant transformation methods.Also identified by the present invention are particular elements withinthese sequences that help to improve the frequency and integrity of DNAintegration. It is an aspect of the present invention that the DNAsequences for any or all of the described transformation elementsoriginate from, or are endogenous to, a plant genome. Thesetransformation elements can be generically described as follows below.

Cleavage site: a function of the cleavage site is to serve as arecognition site for nuclease proteins or protein complexes that mayinclude virD2 and catalyze a single strand DNA nick within the elementduring Agrobacterium-mediated processing.

A desired polynucleotide of interest, which is destined for integrationinto another nucleic acid molecule, may be linked to at least one ofsuch cleavage sites. For example, the desired polynucleotide may beinserted into a plasmid that can be maintained in Agrobacterium and hasbeen engineered to contain these elements, such that the desiredpolynucleotide is ultimately flanked by one or two cleavage sites.

When there exist two cleavage sites, one may be regarded as being mainlyinvolved in initial cleavage, while the other may be regarded astypically supporting final cleavage. The cleavage sites may be identicalin sequence, whereby their functional difference is mediated by specificcharacteristics of flanking DNA. The transfer DNA contains the initialcleavage site upstream from the final cleavage site. Upstream, withrespect to the position of a nucleic acid sequence, means 5′- to the5′-end of any particular nucleic acid sequence. Downstream, with respectto the position of a nucleic acid sequence, means 3′- to the 3′-end ofany particular nucleic acid sequence. All sequences described in thisinvention refer to the DNA strand that corresponds to the transfer DNA.The non-transfer strand contains the inverse complement of the finalcleavage site upstream from the inverse complement of the initialcleavage site.

When a desired polynucleotide is flanked by upstream and downstreamelements, it is advantageous for the elements to be oriented as eitherperfect or imperfect direct repeats of each other.

The sequence of the cleavage site may conform to a consensus sequence,such as that depicted in SEQ ID NO: 84 whereby the sequence of thecleavage site is not identical to an Agrobacterium Right Border or LeftBorder. [A/C/G]-[A/C/T]-[A/C/T]-[G/T]-A- (SEQ ID NO: 84)[C/G]-NNNNNN-A-[G/T]-A-[A/C/T]- [A/G]-TCCTG-[C/G/T]-[A/C/G]-N

The consensus sequence analysis indicates that a DNA sequence that isuseful for transferring one polynucleotide into another can accommodatenucleotide degeneracy, especially at its 5′-terminus.

According to the consensus sequence, a cleavage site may be 25nucleotides in length. The present invention is not limited to thislength, however, but also contemplates longer and shorter cleavage sitesthat function as described herein. That is, regardless of their length,the cleavage sites should facilitate cleavage for subsequent integrationof a desired polynucleotide to which it is linked into another nucleicacid molecule. Accordingly, elements that are 15 nucleotides, 16nucleotides, 17 nucleotides, 18 nucleotides, 19 nucleotides, 20nucleotides, 21 nucleotides, 22 nucleotides, 23 nucleotides, 24nucleotides, 26 nucleotides, 27 nucleotides, 28 nucleotides, 29nucleotides, and 30 nucleotides elements are envisioned as variants tothe 25 nucleotide-long consensus elements described herein.

The functional activity of a putative cleavage site can be tested byinserting it into a “test plasmid” described in the Examples, and usingan Agrobacterium strain carrying the resulting vector to transformplants such as tobacco. Transformation frequencies achieved with thisvector can then be compared to those of conventional benchmark vectorsthat contain at least one Agrobacterium T-DNA Right Border to determinethe efficacy of the putative cleavage site to mediate DNA transfer.

Examples of highly efficient synthetic cleavage sites are shown as SEQID NOs: 8, 9, 11-13, and 15-17. Similarly efficient plant-derivedcleavage sites are depicted in SEQ ID NOs: 28-37 and 85-86. Additionalplant-derived cleavage sites that display at least 5% of the activity ofRight Borders are shown in SEQ ID NOs: 38-50.

Assessment of the functional activity of a putative cleavage site ismore elaborate. Test vectors used for this purpose contain both afunctional site for initial cleavage (or Right Border) and the putativesite for final cleavage as described in the Examples. Upontransformation and molecular analysis, plants are separated in twodifferent classes. One class of plants only contains the transfer DNAdelineated by cleavage sites. This class of transformation events isdesignated “desired.” The second class of plants contains the transferDNA still linked to plasmid backbone sequences. The smaller thepercentage of events belonging to this latter “undesired” class, thebetter the final cleavage site functions in terminating DNA transfer.

In reference to the DNA strand that comprises the transfer DNA, theposition of all DNA regions that are described herein can be identifiedas upstream and downstream of cleavage sites. The regions include:

(1) The UI region. A UI region may include one or more of the followingcharacteristics:

-   -   (a) comprises the first base pair of the initial cleavage site        and at least about 47 base pairs immediately upstream from this        cleavage site,    -   (b) is part of a larger sequence that can be predicted by using        methods described by, e.g., Huang and Kowalski, 2003, to contain        a helical stability that is below the average helical stability,        i.e., the sequence may typically requires less energy for        unwinding than a random DNA sequence comprising the same number        of base pairs,    -   (c) is part of an adenine-rich (>25% adenine resides) sequence,    -   (d) comprises at least one adenine-cytosine dinucleotide.    -   (e) comprises a 45-nucleotide sequence that contains        adenine-rich (>25%) trinucleotides interspaced by nucleotides        that represent, in at least six cases, a cytosine or thymine        (pyrimidine) residue, whereby the most downstream pyrimidine        represents either the first base of the initial cleavage site or        the base at position −4 relative to the initial cleavage site.        See also SEQ ID NOs: 90-97 and 99, and FIGS. 2A and B.    -   (f) may comprise a sequence that shares at least 70% sequence        identity with the overdrive depicted in SEQ ID NO: 88,    -   (g) is not identical to a region that flanks a T-DNA border in        Agrobacterium Ti or Ri plasmids.

The UI region may support or enhance any level of initial cleavageactivity. For instance, a UI region may enhance the initial cleavageactivity by at least 25% compared to the corresponding sequence of theTi or Ri plasmid.

(2) The DI region. A DI region may include one or more of the followingcharacteristics:

-   -   (a) comprises at least 45 base pairs immediately downstream from        the initial cleavage site,    -   (b) comprises a DR domain at a distance of 0-50 base pairs from        the initial cleavage site, wherein the DR domain may comprise        the sequence depicted in SEQ ID NO: 107,    -   (c) optionally contains multiple sequences that are identical or        inverse complementary to SEQ ID 115 (CCCG),    -   (d) is not identical to a region that flanks a T-DNA border in        Agrobacterium Ti or Ri plasmids, and    -   (e) supports or enhances any level of initial cleavage activity.        For instance, a DI region may enhance the initial cleavage        activity by at least 25% compared to the corresponding sequence        of the Ti or Ri plasmid.

(3) The UF region. A UF region may include one or more of the followingcharacteristics:

-   -   (a) comprises at least 40 base pairs immediately upstream from        the final cleavage site,    -   (b) comprises at least 55% adenine or thymine residues        (AT-rich),    -   (c) comprises a sequence that shares at least 70% sequence        identity to the UL domain depicted in SEQ ID NO: 120 or to its        inverse complement within a distance of about 50 base pairs from        the final cleavage site,    -   (d) optionally comprises a putative binding site for integration        host factor with the consensus sequence [A/T]-ATCAANNNNTT-[A/G]        (SEQ ID NO: 129),    -   (e) is not identical to a region that flanks a T-DNA border in        Agrobacterium Ti or Ri plasmids, and    -   (f) supports or enhances any level of initial cleavage activity.        For instance, a UF region may enhance the initial cleavage        activity by at least 25% compared to the corresponding sequence        of the Ti or Ri plasmid.

(4) the AF region. An AF region may include one or more of the followingcharacteristics:

-   -   (a) comprises at least part of the final cleavage site and at        about two to 40 base pairs flanking downstream DNA,    -   (b) comprises at least four tightly linked clusters of two or        more cytosine bases separated by 1-11 other nucleotides,        CCN1-11CCN1-11CCN1-11CC (SEQ ID NO: 122),    -   (c) is not identical to a region that flanks a T-DNA border in        Agrobacterium Ti or Ri plasmids, and    -   (d) supports or enhances any level of initial cleavage activity.        For instance, an AF region may enhance the initial cleavage        activity by at least 25% compared to the corresponding sequence        of the Ti or Ri plasmid.

The cytosine cluster domain is thought to form into tertiaryquadruplexes at slightly acid or neutral pH, in a similar manner asdescribed for mammalian cytosine clusters. See Zarudnaya et al., NucleicAcids Res 31: 1375-1386, 2003, and Neidle and Parkinson, Curr OpinStruct Biol 13: 275-283, 2003. It is possible that the specific foldingassociated with cytosine cluster regions either facilitates or impairsDNA unwinding and/or final cleavage.

The enzymes necessary for implementing Agrobacterium-mediated cleavageinclude virD2 nicking the top strand of this schematic representation.FIG. 4 is a schematic of the transfer cassette within a plasmid for usein Agrobacterium-mediated transformation. The elements are oriented in amanner that corresponds to the sequences described herein. Theirorientation also corresponds to the strand that is transferred fromAgrobacterium to plant cells. It is possible to apply the mirror imageof this arrangement in combination with the inverse complement of thesequences shown herein, whereby “downstream” becomes “upstream” and viceversa. Typically, the first enzyme nick is made by virD2 and accessoryproteins within the initial cleavage site. Sometimes, however, thepertinent enzyme complex does not effectively make a second nick withinthe final cleavage site. In this, situation, therefore, the entire topstrand of the plasmid becomes linearized, and is transferred to theplant cell.

On the other hand, effective nicking at both the initial cleavage siteand the final cleavage site produces a single-stranded DNA molecule thatis terminated by residual portions of the cleavage sites. It is desirousthat this particular DNA molecule be integrated into a plant genome.

Source of Elements and DNA Sequences

Any or all of the elements and DNA sequences that are described hereinmay be endogenous to one or more plant genomes. Accordingly, in oneparticular embodiment of the present invention, all of the elements andDNA sequences, which are selected for the ultimate transfer cassette areendogenous to, or native to, the genome of the plant that is to betransformed. For instance, all of the sequences may come from a potatogenome. Alternatively, one or more of the elements or DNA sequences maybe endogenous to a plant genome that is not the same as the species ofthe plant to be transformed, but which function in any event in the hostplant cell. Such plants include potato, tomato, and alfalfa plants. Thepresent invention also encompasses use of one or more genetic elementsfrom a plant that is interfertile with the plant that is to betransformed.

In this regard, a “plant” of the present invention includes, but is notlimited to angiosperms and gymnosperms such as potato, tomato, tobacco,avocado, alfalfa, lettuce, carrot, strawberry, sugarbeet, cassaya, sweetpotato, soybean, pea, bean, cucumber, grape, brassica, maize, turfgrass, wheat, rice, barley, sorghum, oat, oak, eucalyptus, walnut, andpalm. Thus, a plant may be a monocot or a dicot. “Plant” and “plantmaterial,” also encompasses plant cells, seed, plant progeny, propagulewhether generated sexually or asexually, and descendents of any ofthese, such as cuttings or seed. “Plant material” may refer to plantcells, cell suspension cultures, callus, embryos, meristematic regions,callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen,seeds, germinating seedlings, and microspores. Plants may be at variousstages of maturity and may be grown in liquid or solid culture, or insoil or suitable media in pots, greenhouses or fields. Expression of anintroduced leader, trailer or gene sequences in plants may be transientor permanent.

One or more traits of a tuber-bearing plant of the present invention maybe modified using the transformation sequences and elements describedherein. A “tuber” is a thickened, usually underground, food-storingorgan that lacks both a basal plate and tunic-like covering, which cormsand bulbs have. Roots and shoots grow from growth buds, called “eyes,”on the surface of the tuber. Some tubers, such as caladiums, diminish insize as the plants grow, and form new tubers at the eyes. Others, suchas tuberous begonias, increase in size as they store nutrients duringthe growing season and develop new growth buds at the same time. Tubersmay be shriveled and hard or slightly fleshy. They may be round, flat,odd-shaped, or rough. Examples of tubers include, but are not limited toahipa, apio, arracacha, arrowhead, arrowroot, baddo, bitter casava,Brazilian arrowroot, cassaya, Chinese artichoke, Chinese water chestnut,coco, cocoyam, dasheen, eddo, elephant's ear, girasole, goo, Japaneseartichoke, Japanese potato, Jerusalem artichoke, jicama, lilly root,ling gaw, mandioca, manioc, Mexican potato, Mexican yam bean, oldcocoyam, potato, saa got, sato-imo, seegoo, sunchoke, sunroot, sweetcasava, sweet potatoes, tanier, tannia, tannier, tapioca root,topinambour, water lily root, yam bean, yam, and yautia. Examples ofpotatoes include, but are not limited to Russet Potatoes, Round WhitePotatoes, Long White Potatoes, Round Red Potatoes, Yellow FleshPotatoes, and Blue and Purple Potatoes.

Tubers may be classified as “microtubers,” “minitubers,” “near-mature”tubers, and “mature” tubers. Microtubers are tubers that are grown ontissue culture medium and are small in size. By “small” is meant about0.1 cm-1 cm. A “minituber” is a tuber that is larger than a microtuberand is grown in soil. A “near-mature” tuber is derived from a plant thatstarts to senesce, and is about 9 weeks old if grown in a greenhouse. A“mature” tuber is one that is derived from a plant that has undergonesenescence. A mature tuber is, for example, a tuber that is about 12 ormore weeks old.

In this respect, a plant-derived transfer-DNA (“P-DNA”) border sequenceof the present invention is not identical in nucleotide sequence to anyknown bacterium-derived T-DNA border sequence, but it functions foressentially the same purpose. That is, the P-DNA can be used to transferand integrate one polynucleotide into another. A P-DNA can be insertedinto a tumor-inducing plasmid, such as a Ti-plasmid from Agrobacteriumin place of a conventional T-DNA, and maintained in a bacterium strain,just like conventional transformation plasmids. The P-DNA can bemanipulated so as to contain a desired polynucleotide, which is destinedfor integration into a plant genome via bacteria-mediated planttransformation. See Rommens et al. in WO2003/069980, US-2003-0221213,US-2004-0107455, and WO2005/004585, which are all incorporated herein byreference.

Thus, a P-DNA border sequence is different by 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more nucleotides from aknown T-DNA border sequence from an Agrobacterium species, such asAgrobacterium tumefaciens or Agrobacterium rhizogenes.

A P-DNA border sequence is not greater than 99%, 98%, 97%, 96%, 95%,94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%,80%, 79%, 78%, 77%, 76%, 75%, 74%, 73%, 72%, 71%, 70%, 69%, 68%, 67%,66%, 65%, 64%, 63%, 62%, 61%, 60%, 59%, 58%, 57%, 56%, 55%, 54%, 53%,52%, 51% or 50% similar in nucleotide sequence to an Agrobacterium T-DNAborder sequence.

Methods were developed to identify and isolate transfer DNAs fromplants, particularly potato and wheat, and made use of the border motifconsensus described in US-2004-0107455, which is incorporated herein byreference.

In this respect, a plant-derived DNA of the present invention, such asany of the sequences, cleavage sites, regions, or elements disclosedherein is functional if it promotes the transfer and integration of apolynucleotide to which it is linked into another nucleic acid molecule,such as into a plant chromosome, at a transformation frequency of about99%, about 98%, about 97%, about 96%, about 95%, about 94%, about 93%,about 92%, about 91%, about 90%, about 89%, about 88%, about 87%, about86%, about 85%, about 84%, about 83%, about 82%, about 81%, about 80%,about 79%, about 78%, about 77%, about 76%, about 75%, about 74%, about73%, about 72%, about 71%, about 70%, about 69%, about 68%, about 67%,about 66%, about 65%, about 64%, about 63%, about 62%, about 61%, about60%, about 59%, about 58%, about 57%, about 56%, about 55%, about 54%,about 53%, about 52%, about 51%, about 50%, about 49%, about 48%, about47%, about 46%, about 45%, about 44%, about 43%, about 42%, about 41%,about 40%, about 39%, about 38%, about 37%, about 36%, about 35%, about34%, about 33%, about 32%, about 31%, about 30%, about 29%, about 28%,about 27%, about 26%, about 25%, about 24%, about 23%, about 22%, about21%, about 20%, about 15%, or about 5% or at least about 1%.

Any of such transformation-related sequences and elements can bemodified or mutated to change transformation efficiency. Otherpolynucleotide sequences may be added to a transformation sequence ofthe present invention. For instance, it may be modified to possess 5′-and 3′-multiple cloning sites, or additional restriction sites. Thesequence of a cleavage site as disclosed herein, for example, may bemodified to increase the likelihood that backbone DNA from theaccompanying vector is not integrated into a plant genome.

Any desired polynucleotide may be inserted between any cleavage orborder sequences described herein. For example, a desired polynucleotidemay be a wild-type or modified gene that is native to a plant species,or it may be a gene from a non-plant genome. For instance, whentransforming a potato plant, an expression cassette can be made thatcomprises a potato-specific promoter that is operably linked to adesired potato gene or fragment thereof and a potato-specificterminator. The expression cassette may contain additional potatogenetic elements such as a signal peptide sequence fused in frame to the5′-end of the gene, and a potato transcriptional enhancer. The presentinvention is not limited to such an arrangement and a transformationcassette may be constructed such that the desired polynucleotide, whileoperably linked to a promoter, is not operably linked to a terminatorsequence.

In addition to plant-derived elements, such elements can also beidentified in, for instance, fungi and mammals. See, for instance, SEQID NOs: 173-182. Several of these species have already been shown to beaccessible to Agrobacterium-mediated transformation. See Kunik et al.,Proc Natl Acad Sci USA 98: 1871-1876, 2001, and Casas-Flores et al.,Methods Mol Biol 267: 315-325, 2004, which are incorporated herein byreference. Thus, the new BOA elements may be used to extend the conceptof all-native DNA transformation (Rommens, Trends Plant Sci 9: 457-464,2004) to organisms, such as eukaryotes, other than plants.

When a transformation-related sequence or element, such as thosedescribed herein, are identified and isolated from a plant, and if thatsequence or element is subsequently used to transform a plant of thesame species, that sequence or element can be described as “native” tothe plant genome.

Thus, a “native” genetic element refers to a nucleic acid that naturallyexists in, originates from, or belongs to the genome of a plant that isto be transformed. In the same vein, the term “endogenous” also can beused to identify a particular nucleic acid, e.g., DNA or RNA, or aprotein as “native” to a plant. Endogenous means an element thatoriginates within the organism. Thus, any nucleic acid, gene,polynucleotide, DNA, RNA, mRNA, or cDNA molecule that is isolated eitherfrom the genome of a plant or plant species that is to be transformed oris isolated from a plant or species that is sexually compatible orinterfertile with the plant species that is to be transformed, is“native” to, i.e., indigenous to, the plant species. In other words, anative genetic element represents all genetic material that isaccessible to plant breeders for the improvement of plants throughclassical plant breeding. Any variants of a native nucleic acid also areconsidered “native” in accordance with the present invention. In thisrespect, a “native” nucleic acid may also be isolated from a plant orsexually compatible species thereof and modified or mutated so that theresultant variant is greater than or equal to 99%, 98%, 97%, 96%, 95%,94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%,80%, 79%, 78%, 77%, 76%, 75%, 74%, 73%, 72%, 71%, 70%, 69%, 68%, 67%,66%, 65%, 64%, 63%, 62%, 61%, or 60% similar in nucleotide sequence tothe unmodified, native nucleic acid isolated from a plant. A nativenucleic acid variant may also be less than about 60%, less than about55%, or less than about 50% similar in nucleotide sequence.

A “native” nucleic acid isolated from a plant may also encode a variantof the naturally occurring protein product transcribed and translatedfrom that nucleic acid. Thus, a native nucleic acid may encode a proteinthat is greater than or equal to 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%,91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%, 79%, 78%,77%, 76%, 75%, 74%, 73%, 72%, 71%, 70%, 69%, 68%, 67%, 66%, 65%, 64%,63%, 62%, 61%, or 60% similar in amino acid sequence to the unmodified,native protein expressed in the plant from which the nucleic acid wasisolated.

As used herein, “sequence identity” or “identity” in the context of twonucleic acid or polypeptide sequences includes reference to the residuesin the two sequences which are the same when aligned for maximumcorrespondence over a specified region. When percentage of sequenceidentity is used in reference to proteins it is recognized that residuepositions which are not identical often differ by conservative aminoacid substitutions, where amino acid residues are substituted for otheramino acid residues with similar chemical properties (e.g. charge orhydrophobicity) and therefore do not change the functional properties ofthe molecule. Where sequences differ in conservative substitutions, thepercent sequence identity may be adjusted upwards to correct for theconservative nature of the substitution. Sequences which differ by suchconservative substitutions are said to have “sequence similarity” or“similarity”. Means for making this adjustment are well-known to thoseof skill in the art. Typically this involves scoring a conservativesubstitution as a partial rather than a full mismatch, therebyincreasing the percentage sequence identity. Thus, for example, where anidentical amino acid is given a score of 1 and a non-conservativesubstitution is given a score of zero, a conservative substitution isgiven a score between zero and 1. The scoring of conservativesubstitutions is calculated, e.g., according to the algorithm of Meyersand Miller, Computer Applic. Biol. Sci., 4: 11-17 (1988) e.g., asimplemented in the program PC/GENE (Intelligenetics, Mountain View,Calif., USA).

As used herein, “percentage of sequence identity” means the valuedetermined by comparing two optimally aligned sequences over acomparison window, wherein the portion of the polynucleotide sequence inthe comparison window may comprise additions or deletions (i.e., gaps)as compared to the reference sequence (which does not comprise additionsor deletions) for optimal alignment of the two sequences. The percentageis calculated by determining the number of positions at which theidentical nucleic acid base or amino acid residue occurs in bothsequences to yield the number of matched positions, dividing the numberof matched positions by the total number of positions in the window ofcomparison and multiplying the result by 100 to yield the percentage ofsequence identity.

Methods of alignment of sequences for comparison are well-known in theart. Optimal alignment of sequences for comparison may be conducted bythe local homology algorithm of Smith and Waterman, Adv. Appl. Math. 2:482 (1981); by the homology alignment algorithm of Needleman and Wunsch,J. Mol. Biol. 48: 443 (1970); by the search for similarity method ofPearson and Lipman, Proc. Natl. Acad. Sci. 85: 2444 (1988); bycomputerized implementations of these algorithms, including, but notlimited to: CLUSTAL in the PC/Gene program by Intelligenetics, MountainView, Calif.; GAP, BESTFIT, BLAST, FASTA, and TFASTA in the WisconsinGenetics Software Package, Genetics Computer Group (GCG), 575 ScienceDr., Madison, Wis., USA; the CLUSTAL program is well described byHiggins and Sharp, Gene 73: 237-244 (1988); Higgins and Sharp, CABIOS 5:151-153 (1989); Corpet, et al., Nucleic Acids Research 16: 10881-90(1988); Huang, et al., Computer Applications in the Biosciences 8:155-65 (1992), and Pearson, et al., Methods in Molecular Biology 24:307-331 (1994).

The BLAST family of programs which can be used for database similaritysearches includes: BLASTN for nucleotide query sequences againstnucleotide database sequences; BLASTX for nucleotide query sequencesagainst protein database sequences; BLASTP for protein query sequencesagainst protein database sequences; TBLASTN for protein query sequencesagainst nucleotide database sequences; and TBLASTX for nucleotide querysequences against nucleotide database sequences. See, Current Protocolsin Molecular Biology, Chapter 19, Ausubel, et al., Eds., GreenePublishing and Wiley-Interscience, New York (1995); Altschul et al., J.Mol. Biol., 215:403-410 (1990); and, Altschul et al., Nucleic Acids Res.25:3389-3402 (1997).

Software for performing BLAST analyses is publicly available, e.g.,through the National Center for Biotechnology Information(http://www.ncbi.nlm.nih.gov/). This algorithm involves firstidentifying high scoring sequence pairs (HSPs) by identifying shortwords of length W in the query sequence, which either match or satisfysome positive-valued threshold score T when aligned with a word of thesame length in a database sequence. T is referred to as the neighborhoodword score threshold. These initial neighborhood word hits act as seedsfor initiating searches to find longer HSPs containing them. The wordhits are then extended in both directions along each sequence for as faras the cumulative alignment score can be increased. Cumulative scoresare calculated using, for nucleotide sequences, the parameters M (rewardscore for a pair of matching residues; always >0) and N (penalty scorefor mismatching residues; always <0). For amino acid sequences, ascoring matrix is used to calculate the cumulative score. Extension ofthe word hits in each direction are halted when: the cumulativealignment score falls off by the quantity X from its maximum achievedvalue; the cumulative score goes to zero or below, due to theaccumulation of one or more negative-scoring residue alignments; or theend of either sequence is reached. The BLAST algorithm parameters W, T,and X determine the sensitivity and speed of the alignment. The BLASTNprogram (for nucleotide sequences) uses as defaults a wordlength (W) of11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and acomparison of both strands. For amino acid sequences, the BLASTP programuses as defaults a wordlength (W) of 3, an expectation (E) of 10, andthe BLOSUM62 scoring matrix (see Henikoff & Henikoff (1989) Proc. Natl.Acad. Sci. USA 89:10915).

In addition to calculating percent sequence identity, the BLASTalgorithm also performs a statistical analysis of the similarity betweentwo sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA90:5873-5877 (1993)). One measure of similarity provided by the BLASTalgorithm is the smallest sum probability (P(N)), which provides anindication of the probability by which a match between two nucleotide oramino acid sequences would occur by chance.

BLAST searches assume that proteins can be modeled as random sequences.However, many real proteins comprise regions of nonrandom sequenceswhich may be homopolymeric tracts, short-period repeats, or regionsenriched in one or more amino acids. Such low-complexity regions may bealigned between unrelated proteins even though other regions of theprotein are entirely dissimilar. A number of low-complexity filterprograms can be employed to reduce such low-complexity alignments. Forexample, the SEG (Wooten and Federhen, Comput. Chem., 17:149-163 (1993))and XNU (Clayerie and States, Comput. Chem., 17:191-201 (1993))low-complexity filters can be employed alone or in combination.

Multiple alignment of the sequences can be performed using the CLUSTALmethod of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153) withthe default parameters (GAP PENALTY = 10, GAP LENGTH PENALTY = 10).

Default parameters for pairwise alignments using the CLUSTAL method areKTUPLE 1, GAP PENALTY = 3, WINDOW = 5 and DIAGONALS SAVED = 5.

Transformation Bacterium

Bacteria species and strains other than those of Agrobacterium, e.g.,Agrobacterium tumefaciens, can be used to transform a plant according tothe present invention. For instance, any genera within the familyRhizobiaceae can be used in place of Agrobacterium to transform a plant.For instance, members of the Rhizobium and Phyllobacterium genera can beused to transform a plant according to the present invention. Examplesinclude, but are not limited to, Rhizobium trifolii, Rhizobiumleguminosarum, Phyllobacterium myrsinacearum, SinoRhizobium meliloti,MesoRhizobium loti bacterial strains, which can be used to transform aplant according to the present invention. See Broothaerts et al.,Nature, 433, pp. 629-633, 2005, which is incorporated herein byreference.

Transfer Cassette Embodiments

The present invention does not require the presence of all of theelements described herein in the transfer cassette. Any number ofpermutations of these elements are envisioned. For instance, a transfercassette may comprise a desired polynucleotide, which is flanked bycleavage sites only.

Alternatively, another transfer cassette may comprise a desiredpolynucleotide, which is flanked by cleavage sites and which alsocomprises one or more of the DI and UF regions. The various elements maybe arranged as described herein and as depicted in FIG. 4, but otherarrangements are possible and envisioned by the present invention.

The present invention contemplates, therefore, various permutations ofthe transformation elements disclosed herein, as well as the use ofvariant forms of any of the corresponding sequences disclosed herein.See the section on “variants” below.

It may be desirable to select particular elements, and sequences orvariant sequences that correspond to those elements, which are effectivein transforming a particular plant species. That is, it is possible touse the information disclosed herein, as well as the particularsequences disclosed herein, to optimize transformation efficiencybetween different organisms or plants of different species.

In this regard, the present invention contemplates transforming a plantwith one or more transformation elements that genetically originate froma plant. The present invention encompasses an “all-native” approach totransformation, whereby only transformation elements that are native toplants are ultimately integrated into a desired plant viatransformation. In this respect, the present invention encompassestransforming a particular plant species with only genetic transformationelements that are native to that plant species. The native approach mayalso mean that a particular transformation element is isolated from thesame plant that is to be transformed, the same plant species, or from aplant that is sexually interfertile with the plant to be transformed.

On the other hand, the plant that is to be transformed, may betransformed with a transformation cassette that contains one or moregenetic elements and sequences that originate from a plant of adifferent species. It may be desirable to use, for instance, a cleavagesite, UI, DI, UF, or DF region sequence that is native to a potatogenome in a transformation cassette or plasmid for transforming a tomatoor pepper plant, for example.

The present invention is not limited, however, to native or all-nativeapproach. A transformation cassette or plasmid of the present inventioncan also comprise sequences and elements from other organisms, such asfrom a bacterial species.

Desired Polynucleotides

The origin of the genetic sequences that make up the transformationcassette also may apply to the sequence of a desired polynucleotide thatis to be integrated into the transformed plant. That is, a desiredpolynucleotide, which is located between the primary or initial andsecondary or final cleavage site sequences of the present invention, mayor may not be “native” to the plant to be transformed. As with the othertransformation elements, a desired polynucleotide may be isolated fromthe same plant that is to be transformed, or from the same plantspecies, or from a plant that is sexually interfertile with the plant tobe transformed. On the other hand, the desired polynucleotide may befrom a different plant species compared to the species of the plant thatis to be transformed. Yet, the present invention also encompasses adesired polynucleotide that is from a non-plant organism.

A desired polynucleotide of the present invention may comprise a part ofa gene selected from the group consisting of a PPO gene, an R1 gene, atype L or H alpha glucan phosphorylase gene, an UDP glucoseglucosyltransferase gene, a HOS1 gene, a S-adenosylhomocysteinehydrolase gene, a class II cinnamate 4-hydroxylase gene, acinnamoyl-coenzyme A reductase gene, a cinnamoyl alcohol dehydrogenasegene, a caffeoyl coenzyme A O-methyltransferase gene, an actindepolymerizing factor gene, a Nin88 gene, a Lol p 5 gene, an allergengene, a P450 hydroxylase gene, an ADP-glucose pyrophosphorylase gene, aproline dehydrogenase gene, an endo-1,4-beta-glucanase gene, azeaxanthin epoxidase gene, a 1-aminocyclopropane-1-carboxylate synthasegene, an Rb resistance gene, a Bf2 resistance gene, a Fad2 gene, and anAnt-1 gene. Such a desired polynucleotide may be designed and orientedin such a fashion within a transformation cassette of the presentinvention, so as to reduce expression within a transformed plant cell ofone or more of these genes. See, for instance, Rommens et al. inWO2003/069980, US-2003-0221213, US-2004-0107455, and WO2005/004585,which are all incorporated herein by reference.

Thus, a desired polynucleotide of the present invention may be used tomodify a particular trait in a transformed plant that is normallymanifested by an untransformed plant. For instance, a desiredpolynucleotide may be placed into a transformation cassette of thepresent invention to enhance the health and nutritional characteristicsof the transformed plant or it may be used, for instance, to improvestorage, enhance yield, enhance salt tolerance, enhance heavy metaltolerance, increase drought tolerance, increase disease tolerance,increase insect tolerance, increase water-stress tolerance, enhance coldand frost tolerance, enhance color, enhance sweetness, improve vigor,improve taste, improve texture, decrease phosphate content, increasegermination, increase micronutrient uptake, improve starch composition,and improve flower longevity.

Transformation Vector Embodiments

The present invention does not require the presence of all of theelements described herein in the transformation vector. Any number ofpermutations of these elements are envisioned. For instance, atransformation vector may comprise both a transfer cassette and one ormore UI and AF regions. The elements may be arranged as described hereinand as depicted in FIG. 4, but other arrangements are possible andenvisioned by the present invention.

Transformation of a plant is a process by which DNA is stably integratedinto the genome of a plant cell. “Stably” refers to the permanent, ornon-transient retention and/or expression of a polynucleotide in and bya cell genome. Thus, a stably integrated polynucleotide is one that is afixture within a transformed cell genome and can be replicated andpropagated through successive progeny of the cell or resultanttransformed plant. Transformation may occur under natural or artificialconditions using various methods well known in the art. See, forinstance, METHODS IN PLANT MOLECULAR BIOLOGY AND BIOTECHNOLOGY, BernardR. Glick and John E. Thompson (eds), CRC Press, Inc., London (1993);Chilton, Scientific American, 248)(6), pp. 36-45, 1983; Bevan, Nucl.Acids. Res., 12, pp. 8711-8721, 1984; and Van Montague et al., Proc RSoc Lond B Biol Sci., 210(1180), pp. 351-65, 1980. Plants also may betransformed using “Refined Transformation” and “Precise Breeding”techniques. See, for instance, Rommens et al. in WO2003/069980,US-2003-0221213, US-2004-0107455, WO2005/004585, US-2004-0003434,US-2005-0034188, WO2005/002994, and WO2003/079765, which are allincorporated herein by reference.

Transformation may rely on any known method for the insertion of nucleicacid sequences into a prokaryotic or eukaryotic host cell, including thebacterium-mediated transformation protocols described herein, such asAgrobacterium-mediated transformation, or alternative protocols, such asby viral infection, whiskers, electroporation, heat shock, lipofection,polyethylene glycol treatment, micro-injection, and particlebombardment.

“Activity of the final cleavage site” is determined by comparing thenumber of transformed plants only containing the DNA that is positionedbetween initial and final cleavage site with the total number oftransformed plants. The final cleavage site determines the fidelity ofDNA transfer.

“Activity of the initial cleavage site” is assessed by determining thetransformation frequency of a plasmid carrying this cleavage site.Activity is dependent on both the sequence of the initial cleavage siteitself and the sequence of flanking DNA. Activities are often expressedas a percentage of the activity of conventional Right Borders. Effectiveinitial cleavage sites display at least 50% of the activity of RightBorders if flanked by DNA sequences that support their activity. Usingmethods and strains described in this invention, transformationfrequencies for conventional right borders average about 10-20calli/tobacco explant.

“Bacterium-mediated plant transformation” is the modification of a plantby infecting either that plant or an explant or cell derived from thatplant with a bacterium selected of the group consisting of Agrobacteriumsp., Rhizobium sp., Phyllobacterium sp., SinoRhizobium sp., andMesoRhizobium sp. to transfer at least part of a plasmid that replicatesin that bacterium to the nuclei of individual plant cells for subsequentstable integartion into the genome of that plant cell.

“Cassette” is a DNA sequence that may comprise various genetic elements.

“Cleavage site” is a DNA sequence that is structurally different butfunctionally similar to T-DNA borders. A cleavage site comprises asequence that is nicked when exposed to an enzyme involved inbacterium-mediated plant transformation. It can represent a syntheticsequence that may not be present in the genome of a living organism orit can represent a sequence from a living organism such as a plant,animal, fungus, or bacterium.

“Conventional binary plasmid” is a plasmid that ca be maintained in bothE. coli and A. tumefaciens, and contains T-DNA right and left bordersthat are flanked by at least 10 base pairs of DNA that flank theseelements in Agrobacterium Ti or Ri plasmids.

“Final cleavage site” is a DNA sequence that is structurally orsequentially different, but functionally similar to, the Left Border ofAgrobacterium Ti plasmids by comprising a sequence mediating a secondcleavage reaction and, thus, defining the end point of the transfer DNA.An effective final cleavage site allows transfer of DNA sequences thatdo not include sequences downstream from the final cleavage site, i.e.,plasmid backbone sequences.

“A flanking sequence” is a sequence immediately next to anothersequence.

“Initial cleavage site” is a DNA sequence that is structurally differentbut functionally similar to the Right Border of Agrobacterium Tiplasmids by comprising a sequence that functions as initial cleavagesite and, thus, defines the start point of the transfer DNA. Aneffective initial cleavage site supports or enhances planttransformation compared to a conventional Right Border.

“Non-autonomous transposable element” as used herein is a transposableelement that comprises the ends that are required for transposition butwhich does not encode the protein that is required for transposition.Thus, a non-autonomous transposable element will transpose only if thegene encoding the protein required for transposition is expressed fromeither a different position in the genome or from a plasmid or DNAfragment that resides in the same plant cell.

A “terminal end of a transposable element” is a sequence at the 5′ or 3′end of a transposable element that is required for non-autonomoustransposition. Such sequences may comprise about 100 to about 300nucleotides.

“T-DNA border” is a polynucleotide of approximately 25-base pairs inlength that comprises a sequence that can be nicked when exposed to anenzyme or enzyme complex involved in bacterium-mediated planttransformation and that can define the single stranded DNA fragment thatis transferred from the bacterium to the plant cell.

“UF region” is a DNA sequence that (a) comprises at least 40 base pairsimmediately upstream from either the final cleavage site or left border,(b) comprises at least 55% adenine or thymine residues (AT-rich), (c)comprises a sequence which has at least 70% sequence identity to the ULdomain depicted in SEQ ID NO: 120 or its inverse complement, within adistance of 50 base pairs from the final cleavage site, (d) optionallycomprises a putative binding site for integration host factor with theconsensus sequence [A/T]-ATCAANNNNTT-[A/G] (SEQ ID NO: 129) that ispositioned within 200 base pairs from the final cleavage site or leftborder, (e) is not identical to a region that flanks a T-DNA border inAgrobacterium Ti or Ri plasmids, and (f) supports or enhances activityof the initial cleavage site.

“UI region” is a DNA sequence that (a) comprises the first base pair ofeither the initial cleavage site or right border and at least about 47base pairs immediately upstream from this cleavage site; (b) is part ofa larger sequence that can be predicted by using methods described by,e.g., Huang and Kowalski, 2003, to contain a helical stability that isbelow the average helical stability, i.e., the sequence may typicallyrequires less energy for unwinding than a random DNA sequence comprisingthe same number of base pairs; (c) is part of an adenine-rich (>25%adenine resides) sequence; (d) comprises at least one adenine-cytosinedinucleotide; (e) comprises a 45-nucleotide sequence that containsadenine-rich (>25%) trinucleotides interspaced by nucleotides thatrepresent, in at least six cases, a cytosine or thymine (pyrimidine)residue, whereby the most downstream pyrimidine represents either thefirst base of the initial cleavage site or the base at position −4relative to the initial cleavage site. See also SEQ ID NOs: 199-208, andFIGS. 2A and B; (f) may comprise a sequence with at least 70% sequenceidentity to the overdrive depicted in SEQ ID NO: 88; (g) is notidentical to a region that flanks a T-DNA border in Agrobacterium Ti orRi plasmids; and (h) supports or enhances activity of the initialcleavage site.

“UI-like region” is a sequence that resembles a UI region but differs inthat it (1) represents Agrobacterium sequences flanking a Right Border,or (2) impairs the efficacy of a Right Border or cleavage site. TheUI-like region may reduce transformation frequencies to less than thatof a conventional Right order-flanking DNA sequence. For instance, itmay reduce a transformation frequency to less than about 25%.

“Transformation vector” is a plasmid that can be maintained inAgrobacterium, and contains at least one Right Border or initialcleavage site. Infection of explants with Agrobacterium strains carryinga transformation vector and application of transformation procedureswill produce transformed calli, shoots, and/or plants that contain atleast part of the transformation vector stably integrated into theirgenome. The vector may comprise a selectable marker to aididentification of plants that have been stably transformed.

A “selectable marker” is typically a gene that codes for a protein thatconfers some kind of resistance to an antibiotic, herbicide or toxiccompound, and is used to identify transformation events. Examples ofselectable markers include the streptomycin phosphotransferase (spt)gene encoding streptomycin resistance, the phosphomannose isomerase(pmi) gene that converts mannose-6-phosphate into fructose-6 phosphate;the neomycin phosphotransferase (nptII) gene encoding kanamycin andgeneticin resistance, the hygromycin phosphotransferase (hpt or aphiv)gene encoding resistance to hygromycin, acetolactate synthase (als)genes encoding resistance to sulfonylurea-type herbicides, genes codingfor resistance to herbicides which act to inhibit the action ofglutamine synthase such as phosphinothricin or basta (e.g., the bargene), or other similar genes known in the art.

A “variant,” as used herein, such as a variant of any of the nucleicacid molecules or polypeptides described herein, is understood to mean anucleotide or amino acid sequence that deviates from the standard, orgiven, nucleotide or amino acid sequence of a particular gene orprotein. The terms, “isoform,” “isotype,” “homolog,” “derivative,” and“analog” also refer to “variant” forms of a nucleotide or an amino acidsequence. An amino acid sequence that is altered by the addition,removal or substitution of one or more amino acids, or a change innucleotide sequence, may be considered such a “variant” sequence. Thevariant may have “conservative” changes, wherein a substituted aminoacid has similar structural or chemical properties, e.g., replacement ofleucine with isoleucine. A variant may have “nonconservative” changes,e.g., replacement of a glycine with a tryptophan. Analogous minorvariations may also include amino acid deletions or insertions, or both.Guidance in determining which amino acid residues may be substituted,inserted, or deleted may be found using computer programs well known inthe art such as Vector NTI Suite (InforMax, Md.) software.

The present invention encompasses a variant that has one or more pointmutations compared to one of the sequenced disclosed herein. Forinstance, any one of the cleavage site sequences depicted by SEQ ID NOs:8, 9, 11-13, 15-17, 28-37, 38-51, 85-86, 189, 194-196, may comprise oneor more point mutations. That mutated variant may then be readily testedfor activity or its effect on transformation efficiency, simply byreplacing the original sequence with the mutated version and determiningwhether the sequence is cleaved and whether the efficiency oftransformation is maintained, increased, or decreased.

Similarly, any of the sequences disclosed herein for a UI, DI, UF, or AFregion may be mutated and similarly tested for activity and effect ontransformation efficiency.

Thus, the present invention is not limited to the sequences disclosedherein that correspond to a particular transformation element. Rather,actual sequences can be used in any permutation to create useful andeffective transformation cassettes and plasmids, or one or more of thecomponent transformation elements may be mutated, tested for activity,and then incorporated into a desired transformation cassette or plasmid.

In this regard, a variant sequence of the present invention, such as avariant of a cleavage site or UI, DI, UF, or AF region, may be afunctional homolog of a particular sequence. By this it is understoodthat a cleavage site that is a variant of, for instance, one of SEQ IDNOs: 8, 9, 11-13, 15-17, 28-37, 38-51, 85-86, 189, 194-196, but whichstill can be cleaved by an enzyme, is a functional derivative of theoriginal sequence. By the same token, the present invention encompassesfunctional derivatives of any of all of the transformation elements,e.g., UI, DI, UF, and AF regions, disclosed herein.

A variant sequence of the present invention also encompasses shorter andlonger sequences of those specific sequences disclosed herein. Forinstance, the cleavage site sequence depicted in SEQ ID NO: 8 may bepositioned within a larger fragment of DNA, which may or may not beplant DNA. The subsequently larger fragment may then be inserted into atransformation cassette or plasmid. Thus, the present invention is notlimited to manipulating only a polynucleotide that consists of aparticular SEQ ID NO: sequence. Accordingly, one may use one of thesequences of the present invention, such as SEQ ID NO: 8, to identifyand isolate another sequence homolog from a plant or any other organismgenome. It may be desirable to isolate a fragment of that genomic DNAthat includes sequences flanking the homolog of interest. The largerfragment, within which is included the same or similar homolog to adesired sequence described herein, may then be tested according to themethods described herein for functional activity, i.e., it may be testedto determine what effect, if any, it has on transformation efficiency incomparison to a control system that does not include the larger fragmenthomolog. Thus, a “variant” of any of the sequences described herein, notonly that exemplified by SEQ ID NO: 8, be it a sequence for a cleavagesite or for a UI, DI, UF, or AF region, for instance, encompasses longerversions of the corresponding sequences disclosed herein.

Conversely, a “variant” of the present invention also encompassespolynucleotides that are shorter than a corresponding sequence of thepresent invention. That is a variant polynucleotide may be “a part of” asequence disclosed herein. It is well within the purview of the skilledperson to make truncated versions of a sequence disclosed herein. Forinstance, the present invention contemplates truncating a cleavage site,for instance, by any number of nucleotides and then testing thatcleavage site for activity. For example, one may truncate the cleavagesite depicted in SEQ ID NO: 8 by removing the 5 nucleotides from the3′-end of SEQ ID NO: 8 and then test that truncated fragment of SEQ IDNO: 8 for cleavage activity. That is, one may test to see if a pertinentenzyme can still cleave the truncated SEQ ID NO: 8, by virtue ofassaying for the cleavage directly or by ascertaining the effect of thetruncated SEQ ID NO: 8 on transformation efficiency compared to acontrol system, which employs the full-length sequence of SEQ ID NO: 8.

A truncation may be made at either end or within a particular sequencedescribed herein. Thus, a variant that comprises a part of, say, SEQ IDNO: 8, may be any part of SEQ ID NO: 8. SEQ ID NO: 8 is only used hereas an example. Any of the sequences disclosed herein may be truncated insuch fashion and then tested for subsequent activity and/ortransformation efficiency.

Any of the sequences described herein can be chemically synthesized.That is, it may not be necessary to physically isolate and purify aparticular sequence from an organism genome prior to use. For thisreason, a “truncated” version of a sequence described herein may beobtained by terminating chemical synthesis at any desired time pointduring manufacture.

Thus, a variant that is a “part of” a sequence disclosed herein may bemade directly using chemical synthesis techniques rather than physicallyobtained from the actual polynucleotide in question. The same strategyapplies for the longer variant forms: it is possible to chemicallysynthesize a polynucleotide, within which comprises a particularsequence described herein.

The following examples serve to illustrate various embodiments of thepresent invention and should not be construed, in any way, to limit thescope of the invention.

All references cited herein, including patents, patent application andpublications, are hereby incorporated by reference in their entireties,where previously specifically incorporated or not.

Having now fully described this invention, it will be appreciated bythose skilled in the art that the same can be performed within a widerange of equivalent parameters, concentrations and conditions, withoutundue experimentation. This application is intended to cover anyvariations, uses, or adaptations of the invention, following in generalthe principles of the invention, that include such departures from thepresent disclosure as come within known or customary practice within theart to which the invention pertains and as may be applied to theessential features hereinbefore set forth.

EXAMPLE 1 Initial Cleavage Sites

Isolated plant sequences were used as effective initial cleavage sitesto mediate DNA transfer as well as effective final cleavage sites tolimit the co-transfer of vector backbone sequences. In fact, backbonetransfer frequencies with plant-derived cleavage sites that were linkedto upstream AT-rich regions and downstream C-cluster regions were lowerthan obtained with conventional Left Borders. The DNA sequencesdescribed herein permits the construction of efficient all-nativetransfer DNAs that can be used for the production of intragenic potato,tomato, and alfalfa plants.

Cleavage Sites

Initial cleavage sites function in the initiation of DNA transfer andare positioned in transformation plasmids at the junction of (i) the5′-end of sequences destined for transfer from Agrobacterium to plantcells (the transfer DNA) and (ii) plasmid backbone sequences requiredfor maintenance of the plasmid in Agrobacterium. Their sequences deviatefrom that of the Agrobacterium Right Borders shown in SEQ ID NOs: 1-7denoted Rb01-Rb07, respectively. Examples of synthetic initial cleavagesites are depicted in SEQ ID NOs: 8-13, which are denoted Sy01-Sy13.

To test the functional activity of putative initial cleavage sites, suchsequences were linked to (i) an upstream 109-base pair AgrobacteriumpTi15955 sequence preceding the conventional right border (SEQ ID NO:1), and (ii) a DI region shown in SEQ ID NO: 22. This construct wasinserted into a plasmid containing an expression cassette for theneomycin phosphotransferase (nptII) selectable marker gene.Agrobacterium strains carrying the resulting ‘single element’ testvector were subsequently used to infect tobacco explants.

Two weeks after infection, the average numbers of calli per explant werecompared to those produced with a control plasmid containing Rb01(15.3±0.5). As shown in FIG. 1, all putative cleavage sites enabled DNAtransfer. However, base substitutions C6A, A13C, C19G, C20G, and T21A ofcleavage site Sy03, Sy07, Sy11, Sy12, and Sy13, respectively, loweredtransformation frequencies more than five-fold.

Sequence requirements for initial cleavage were further determined bytesting the efficacy of plant sequences that resemble the Agrobacteriumconsensus (FIG. 1). In addition to the cleavage site of a previouslycharacterized Solanum tuberosum (potato) P-DNA (Rommens et al., PlantPhysiol 135: 421-431, 2004), designated here as St01 (SEQ ID NO: 23), alarge number of new elements were identified by searching publiclyavailable databases including those maintained by “The National CenterFor Biotechnology Information” using, for instance, the “Motif Alignmentand Search Tool” (Bailey and Gribskov, J Comput Biol 5: 211-21, 1998)and “advanced BLASTN” (Altschul et al., Nucleic Acids Res 25: 3389-3402,1997). Search motifs included CAGGATATATNNNNNNGTA, (SEQ D NO: 130)using parameters such as (i) penalty for nucleotide mismatch =−1, and(ii) expect=105. All hits were further analyzed to determine whetherthey uncovered sequences resembling CON1 and/or CON2. Additionaldatabases that were searched include those covering Solanaceae(www.sgn.cornell.edu/), Compositae (compositdb.ucdavis.edu/), andMedicago truncatula (www.genome.ou.edu/medicago.html). Alternatively,border-like sequences were isolated from genomes by employing apolymerase chair reaction (PCR) approach. For this purpose, plant DNAs(2 μg), partially digested with SauIIIA, were ligated with 192-bpBamHI-EcoRV fragments of pBR322. The resulting DNAs were used astemplates for amplification with a degenerate primer, SEQ ID NO: 24, andan anchor primer, SEQ ID NO: 25, with 49° C. annealing temperature and2.5-minute extension time. Subsequent PCRs were performed with theamplified DNAs ligated with pGEM-T as templates using the degenerateprimer together with either SP6 or T7 primers at a slightly higherannealing temperature (52° C.). The products of these reactions wereinserted into pGEM-T and sequenced to design primers for conventionalinverse PCRs to determine the actual putative cleavage site sequences.

Among the new plant-derived cleavage sites, only the Arabidopsisthaliana At01 element (SEQ ID NO: 26) fully matched the Agrobacteriumright border consensus.

However, this element displayed only 65% of the activity of theconventional Right Border Rb02. The lower activity of At01 suggests thatthe guanine base at position +4 (G4) is not as effective as T4.

Most cleavage sites contain at least one mismatch with the consensussequence of Agrobacterium Right Borders (CON1) shown in FIG. 1 anddepicted in SEQ ID NO: 27: [A/C/G][A/T][A/T][G/T]AC[A/C/ (SEQ ID NO: 27)T]N[C/G/T][A/C/G][A/C/G][A/C/ G]ATATATCC TG[C/T]CA

Despite the presence of one to three mismatches with CON1, the followingcleavage site displayed at least 50% activity. This result demonstratesthat Agrobacterium appears to not have exploited the full potential ofborder sequence variation. See SEQ ID NOs: 28-37. Other cleavage sitesinclude those depicted in SEQ ID NOs: 38 and 39. Cleavage sites thatdisplayed activities between about 50% and 5% are depicted in SEQ IDNOs: 40-50.

Mismatches and/or point deletions in 31 cleavage site-like sequencesfrom a variety of plant species resulted in either low activity (lessthan about 5%) or no detectable activity at all. See the sequencesdepicted in SEQ ID NOs: 38, 39, 52-83, 193, and 197.

By comparing tested Right Borders, cleavage sites, and cleavagesite-like elements, a consensus, CON2, was identified. See FIG. 1D andSEQ ID NO: 84: 5′-[A/C/G]-[A/C/T]-[A/C/T]-[G/T]- (SEQ ID NO: 84)A-[C/G]-NNNNNN-A-[G/T]-A-[A/C/T]- [A/G]-TCCTG-[C/G/T]-[A/C/G]-N.

Mismatches that reduced transformation frequencies most dramaticallyinclude, apart from those mentioned above, A5G and C6G.

The high activity of tomato Le01 prompted us to search for homologs inrelated plant species. Identification of identical copies in pepper(Ca01, SEQ ID NO: 85) and potato (St02, SEQ ID NO: 86) DNAs indicatesthat a single cleavage site can be used for all-native DNAtransformation of at least three different Solanceous plant species,potentially facilitating the governmental approval process. We alsoidentified a potato homolog of tomato Le05. However, the reducedefficacy of that cleavage site may limit its applicability for planttransformation.

To obtain an effective cleavage site for use in maize, we can modifyZm01 (SEQ ID NO: 50) by replacing a single base pair. Substitution ofthe guanine residue at position 3 by a thymine residue will yield aZm01-derived cleavage site, designated Zm01M1 (SEQ ID NO: 51).

Similarly, an effective Brassica cleavage site can be obtained bymodifying SEQ ID NO; 52 to create SEQ ID 189, or by modifying SEQ ID NO:197 to produce SEQ ID NO: 198.

Efficient cleavage sites for soybean can be obtained by modifying Gm01(SEQ ID NO: 38) and Gm02 (SEQ ID NO: 39) to create Gm01M1 (SEQ ID NO:195) and Gm02M1 (SEQ ID NO: 196), respectively.

EXAMPLE 2 Spacing Requirements for an Extended Overdrive Domain

The effective test plasmid pSIM551 contained St02 linked to thesequences that contain a 31-bp fragment of pTi15955 inserted betweennovel sequences. The DNA region comprising this sequence and the firstnucleotide of Le01 is the part of SEQ ID NO: 87 depicted in SEQ ID NO:199, and represents a UI region. This arrangement placed the cleavagesite for potato at a distance of 12 base pairs from the overdrive, anelement that was reported to promote DNA transfer (van Haaren et al.,1987) and depicted in SEQ ID NO: 88.

Although the overdrive element is believed to function in a positionindependent manner (Shurvinton and Ream, 1991), we found that a singlebase pair insertion between St02 and upstream DNA (SEQ ID NO: 89) inpSIM578 reduced transformation frequencies of pSIM579 about two-fold(FIG. 3A). Furthermore, the 5′-CAA trinucleotide insertion into the UIregion of pSIM579 (SEQ ID NO: 90) had an even greater negative effect onthe efficacy of transformation, lowering it to 35%.

To study the molecular basis of the apparent overdrive-St02 spacingrequirement, we compared the UI region of pSIM551 (SEQ ID NO: 199) withcorresponding T-DNA flanking regions of Agrobacterium plasmids (SEQ IDNOs: 91-97 shown in SEQ ID NOs: 200-206). The aligned sequencesgenerally contained cytosine or thymine residues at conservedfour-nucleotide intervals, separated by adenine-rich (46%) trinucleotidesegments (FIG. 3A). This arrangement resulted in a high occurence of ACdinucleotide repeats (27%) approaching that of the overdrive elementitself (42%).

Whereas the sequences upstream from (1) the Right Borders ofAgrobacterium plasmids and (2) the UI region of pSIM551 comprised atleast six pyrimidine residues at conserved positions, the impairedactivity of pSIM578 and 579 was correlated with UI regions thatcontained five and four such residues, respectively (FIG. 2A).Additional evidence for the importance of correctly spaced pyrimidineswas obtained by analyzing the UI region of pSIM580, which contained thepentanucleotide 5′-ACCAA insertion between St02 and upstream DNA (partof SEQ ID NO: 98 shown in SEQ ID NO: 207). Maintenance of sixpyrimidines at conserved positions in this plasmid was associated withthe same DNA transfer activity as that of the original vector pSIM551(FIG. 2A).

To further test the functional significance of correctly spacedpyrimidines, the UI region of pSIM551 was replaced by a sequence thatdisplayed 77% identity with the Agrobacterium pRi2659 sequences upstreamfrom the right border (Hansen et al., 1992). Immediate linkage with St02yielded a UI region (part of SEQ ID NO: 99 shown in SEQ ID NO: 208) inpSIM844 that supported high transformation frequencies (125%) (FIG. 2A).However, disruption of the pyrimidine spacing by a single base pairinsertion resulted in a UI-derived region of pSIM827 (part of SEQ ID NO:100 shown in SEQ ID NO: 207) that lowered transformation frequencies to7%.

Having correlated the original spacing of pyrimidines with efficient DNAtransfer, we now also tested the functional relevance of adenine-richspacers. For this purpose, the UI region of pSIM551 was replaced with atomato DNA fragment carrying nine pyrimidines at conserved positions butlacking a high percentage of adenine residues in the intervals (part ofSEQ ID NO: 101 shown in SEQ ID NO: 210). The resulting vector pSIM581displayed only 15% of the transformation efficacy of pSIM551, indicatingthat adenine-rich intervals or AC repeats play a role in the functionalactivity of the UI region (FIG. 2A).

Since adenine-rich DNA is often associated with low helical stabilityregions, we determined the helical stability profile of pSIM551 usingWEB THERMODYN (Huang and Kowalski, 2003). This analysis identified a120-bp sequence immediately upstream from the St02 cleavage site andincluding the UI region to represent the lowest helical stability regionof the pSIM551 backbone (FIG. 2B and data not shown). The association ofan easily unwound DNA region immediately upstream from the RBA may befunctionally relevant because Agrobacterium Ti and Ri plasmids containsimilar low helical stability regions at their Right Borders. Forinstance, pTiC58 contains a 120-bp region preceding the border with astability of 116 kcal/mol. Analogous to the association of low helicalstability regions with the initiation of plasmid replication (Natale etal., 1993), these upstream DNAs may be involved in the initiation of DNAtransfer. We conclude that the overdrive is part of a larger UI-likeregion that is conserved among Agrobacterium plasmids. This domainsupports St02-mediated DNA transfer if correctly spaced relative to theinitial cleavage site, and may be involved in local DNA unwinding. Thesequence that comprises the first nucleotide of the initial cleavagesite and at least about 47 nucleotides of flanking upstream DNA isdesignated UI region.

EXAMPLE 3 The Role of Sequences Downstream from Initial Cleavage Sites

Given that upstream DNA sequences adjacent to the border regioninfluenced transformation efficacy, we sought to test the effect ofdownstream modifications. As shown in FIG. 2C, analyses of the sequencesdownstream from Right Borders and depicted in SEQ ID NOs: 102-106identified decamers that shared the consensus5′-[A/C/T]-[A/C]-[A/C/T]-[A/G/T]- (SEQ ID NO: 107)[A/T]-T-[A/C]-G-[G/T]-[G/T]with the 5′-part of the overdrive, and were positioned at a distance ofone to 27 nucleotides from the right border. This “downstream from rightborder” (DR) domain was also identified in both the potato-derivedtransfer DNA (Rommens et al., 2004) of pSIM108 (SEQ ID 108) and DIregions of test vectors such as pSIM551 (SEQ ID NO: 109) (FIG. 2C). Anincrease in the spacing between Le01 and DR domain from 24 nucleotidesin the DI region of pSIM551 to 48 nucleotides in pSIM920 (SEQ ID NO:110) lowered transformation frequencies by 40% (FIG. 3C), indicatingthat the supporting function of DR domain on border activity is spacingdependent.

Because downstream DNA sequences represent the actual transfer DNA thatis intended for plant transformation, we replaced the original bacterialsequences of pSIM551 with two unique potato DNA fragments. ThepSIM551-derivative pSIM793 (SEQ ID NO: 113), which contained a DR domainat 27 nucleotides from Le01 yielded about the same transformationfrequency as pSIM551. In contrast, the potato DNA fragment of pSIM582(SEQ ID NO: 112), which contained a DR domain with several mismatches tothe consensus, displayed only 59% activity. Interestingly, replacementof Le01-flanking DNA sequences by an alfalfa DNA fragment that containedtwo different DR domains (SEQ ID NO: 114) triggered unusually hightransformation frequencies for the resulting vector pSIM843 (168%) (FIG.3C). This high activity may also be due, in part, to the specificsequence of the upstream DNA of pSIM843, which contains eight 5′-GCCC(SEQ ID NO: 115) repeats. We conclude that sequences flanking rightborder alternatives play an important role in supporting plant DNAtransfer. These sequences comprise upstream ACR and downstream DRdomains.

EXAMPLE 4 Substitution of Left Borders by Right Border Alternatives

The above-described studies had shown that CON2-matching 25-bp elementsfunction as effective right border alternatives if flanked by sequencesthat support their activity. As shown in SEQ ID NOs: 116-119, functionaldifferences exist, and there is divergent sequence organization, at andaround, the left and right border sites. In contrast to right borders,for instance, left borders:

(1) are preceded by AT-rich DNAs each comprising an “upstream from leftborder” (UL) domain on either DNA strand with the consensus sequenceA[C/T]T[C/G]A[A/T]T[G/T][C/T][G/ (SEQ ID NO: 120)T][C/G]A[C/T][C/T][A/T];

(2) share a more conserved consensus sequence:5′-[A/G]TTTACA[A/C/T][A/C/T][A/C/ (SEQ ID NO: 121)T][C/G]AATATATCCTGCC[A/G];and

(3) are linked to downstream plasmid backbone DNA by cytosine clusters(“C-clusters”) that conform to the consensus CCN1-11CCN1-11CCN1- (SEQ IDNO: 122) (FIG. 3A). 11CC

Direct evidence for the role of the C-cluster organization in supportingleft border activity was obtained by comparing the fidelity of DNAtransfer for pSIM831 and 829. Both vectors contained an expressioncassette for the nptII gene preceded by DNA regions comprising St02 asright border alternative, and were confirmed to support the same hightransformation frequencies as pSIM551 (data not shown). The vectors alsocontained almost identical DNA regions for secondary cleavage, shown inSEQ ID NOs: 123 and 124, respectively, which differed only in thatpSIM829 contained a 10-bp insertion in the fourth left border-associatedC-cluster (FIG. 3B).

The effect of this small change was assessed by classifying regeneratedshoots in three groups based on PCR analyses. The first ‘T’ group onlycontained the intended transfer DNA, and would therefore be predicted tohave arisen from primary cleavage events at the right border followed bysecondary cleavage at the left border. Plants containing both thetransfer DNA and additional backbone DNA sequences were classified in asecond “TB” group, and most likely represented events where the secondcopy of the border alternative failed to function in terminating DNAtransfer. The third ‘B’ group of events only contained backbone DNA, andprobably arose from initial cleavage reactions at the second St02 copy.This genotype classification demonstrated that pSIM831 was more thantwice as effective as pSIM829 (41% vs. 17%) in producing ‘T’ events(FIG. 3B).

The sequence comprising at least part of the final cleavage site and atleast one nucleotide of flanking downstream DNA, and comprising aC-cluster region, is designated AF region.

Efficacy of right border alternatives as sites for secondary cleavagewas studied by testing pSIM108 and 843B. The vectors contained St01 andMs01, respectively, as right border alternative. The downstream regionof pSIM108, shown in SEQ ID 125, contained (1) AT-rich (62%) DNA (SEQ IDNO: 184), comprising a putative binding site for integration host factorwith the consensus 5′-[A/T]-ATCAANNNNTT-[A/G] (SEQ ID NO: 129), andderived from the terminator of the potato ubiquitin-3 gene (Garbarino etal., 1994) containing a UL domain, and (2) a second copy of St01associated with plasmid backbone DNA comprising five C-clusters (SEQ IDNO: 125).

Similarly, the DNA region intended for secondary cleavage in pSIM843B(SEQ ID NO: 126) contained a second copy of Ms01 preceded by an AT-rich(87%) alfalfa DNA fragment, and followed by downstream C-clusters (FIG.3B). Vector pSIM401, which contained the extended left border region ofpTiC58, was used as control. PCR genotyping demonstrated that bothpSIM108 and 843B yielded even higher frequency of backbone-freetransformation events (41.1 and 33.9%) than obtained with the control(26.0%), thus indicating that right border alternatives can be used toreplace left borders.

A modification of pSIM843B that both eliminated the UL domain andaltered the spacing of C-clusters yielded a UF region that lowered thefrequency of desired ‘T’ transformation events for the resulting vectorpSIM849 (SEQ ID NO: 127) to 10.2% (FIG. 3B). This reduced frequency wasassociated with an about two-fold increased transfer of DNAs that arestill attached to their vector backbones, indicating that themodifications of flanking DNA interfered with effective secondarycleavage at the second Ms01 copy. Similar alterations of the UF regionof pSIM108 resulted in a sequence (SEQ ID NO: 127) that reducedtransformation efficacy about four-fold (FIG. 3B).

Sequences of UF regions of pSIM108, pSIM843B and pSIM781 are depicted inSEQ ID NOs: 184-186.

Collectively, this data demonstrate that right border alternatives canbe used to replace left borders if associated with upstream UL domainand downstream C-clusters. Even small changes in this organization werefound to have a profound effect on the frequency of backbone-free planttransformation. Replacement of the internal nptII gene expressioncassette of pSIM843B by alfalfa DNA would make it possible to produceintragenic alfalfa plants.

The full region of pSIM843B for efficient initial cleavage comprises UIregion, Ms01, and DI region, and is shown in SEQ ID NO: 131. The fullregion of pSIM843B for efficient final cleavage comprises UF region,Ms01, and AF region, and is shown in SEQ ID NO: 132.

EXAMPLE 5 Cleavage Sites from Eukaryotes Other than Plants

In addition to plant-derived cleavage sites, such elements can also beidentified in, for instance, fungi and mammals. See, for instance, SEQID NOs. 173-182. Several of these species have already been shown to beaccessible to Agrobacterium-mediated transformation (Kunik et al., ProcNatl Acad Sci USA 98: 1871-1876, 2001; Casas-Flores et al., Methods MolBiol 267: 315-325, 2004). Thus, the new elements may be used to extendthe concept of all-native DNA transformation (Rommens, Trends Plant Sci9: 457-464, 2004) to eukaryotes other than plants.

The present invention also contemplates methods for identifying otherpolynucleotide sequences that can be used in place of the specificsequences described herein. For instance, it is possible to identifypolynucleotide sequences that can replace cleavage sites, as well aspolynucleotide sequences that can replace the regions that are upstreamand downstream of the cleavage sites.

A sequence that is upstream of the cleavage site is removed and adifferent polynucleotide is inserted. The sequence of the differentpolynucleotide may or may not be known. With all the other elements inplace to facilitate appropriate transformation in the transfer cassetteand plasmid, the insertion is tested to determine if the differentpolynucleotide facilitates transformation. The assay makes it possibleto identify alternative polynucleotide sequences that can be used tobuild an effective transfer cassette. Accordingly, one may transform aplant with a transformation plasmid in which a candidate polynucleotidesequence has been inserted in place of one of the established sequencesdescribed herein. Successful plant transformation is monitored and theinserted DNA further characterized.

Hence, various elements described herein can be replaced with candidateDNA sequences to test whether those candidate DNA sequences are usefulas alternative functional elements for successful plant transformation(see FIG. 4).

EXAMPLE 6 Alternative Final Cleavage Sites

Instead of using Left Borders or cleavage sites that conform to SEQ IDNO: 84, it is also possible to use the sequence depicted in SEQ ID NO:133, or a fragment thereof, as a final cleavage site. Actual singlestranded DNA cleavage often occurs between the 14th and 15th nucleotide.However, it is also possible that transferred DNA comprises either moreor less than 14 nucleotides of SEQ ID NO: 133.

Binary vectors that contain (1) either a Right Border or initialcleavage site upstream from a polynucleotide and (2) SEQ ID NO: 133 asfinal cleavage site downstream from this polynucleotide can be used toefficiently transfer the polynucleotide, often still flanked by aboutthree base pairs of the 3′-terminus of the Right Border or initialcleavage site and about 14 base pairs (CCCGAAAAACGGGA) (SEQ ID NO: 191)of the alternative final cleavage site. Together, the transferredsequence can be designated “transfer DNA.”

Given the size of plant genomes, only plant species with very smallgenomes may not contain the 14 base pair sequence of SEQ ID NO: 133 thatis transferred, as part of the transfer DNA, from the binary vector tothe plant cell. For instance, Arabidopsis contains ACCGAAAAACGGGA (SEQID NO: 192)

instead of SEQ ID NO: 191. The mismatch at position “1” would representa single point mutation, which is acceptable for all-native DNAtransformation because point mutations occur spontaneously in plantgenomes. Furthermore, it is possible to use parts of SEQ ID NO: 133 asalternative final cleavage site. For instance, SEQ ID NO: 134 to SEQ IDNO: 137,or functional fragments thereof, may be used.

Interestingly, the fidelity of DNA transfer with vectors that containSEQ ID NO: 133 as an alternative final cleavage site is higher thansimilar vectors that contain a conventional Left Border region instead.Table 1 shows the genotypes of tobacco plants derived from an infectionwith Agrobacterium LBA4404 carrying specific plasmids. Plasmid pSIM794contains an expression cassette for the neomycin phosphotransferase(nptII) gene inserted between a conventional Right Border and SEQ ID NO:133. Plasmid pSIM795 contains the same plasmid except that SEQ ID NO:133 is positioned in the inverse complementary (antisense) position. Thebenchmark vector contains conventional Left and Right Borders (pSIM109),and the previously discussed pSIM1008 was used as control vector. SeeTable 1. The use of alternative final cleavage site makes it unnecessaryto use associated UF and AF regions.

EXAMPLE 7 T-DNA-Delivered Transposon-Based Transformation

Instead of using either borders or cleavage sites as sequences thatdefine the ends of the polynucleotide intended for plant transformation,it is also possible to use the termini of plant transposable elements.Until now, transposon-based transformation systems were based on eitherprotoplast transformation (Houba-Herin et al., 1994) or geminivirusvectors (Laufs et al., 1990; Shen and Hohn, 1992; Wirtz et al., 1997;Shen et al., 1998). Both these systems are extremely inefficient, andhave not been pursued for commercial purposes. In contrast toconventional transposon-based transformation, we employ the transfer DNAto deliver the transposable element into the plant nucleus. Excisionfrom the transferred DNA, followed by integration into the plant genome,results in effective plant transformation.

The plasmid used to demonstrate the efficacy of T-DNA-deliveredtransposon-based (TDTB) transformation contains the conventional Leftand Right Border regions of Agrobacterium. Between these border regions,the following elements were inserted: (1) an expression cassette for thetransposase gene of the maize transposable element Ac (SEQ ID NO: 138),(2) a non-autonomous transposable element designated ‘transposon’comprising an expression cassette for the neomycin phosphotransferase(nptII) gene positioned between the 5′ and 3′ ends of the Ac elementdepicted in SEQ ID NOs: 139 and 140, and (3) an expression cassette forthe cytosine deaminase (coda) gene. See FIG. 5. Transgenic plants werecreated as follows:

Tobacco explants (4,500) were infected with an Agrobacterium straincarrying the plasmid described above. The infected explants wereco-cultivated and transferred to medium containing kanamycin (100 mg/L)to select for plant cells expressing the nptII gene. After one month,shoots were transferred to fresh media that also contained the non-toxic5-fluorocytosine (5-FC). Stable integration of the entire transfer DNAwould result in constant expression of the codA gene and subsequentconversion of 5-FC into toxic 5-fluorouracil (5-FU). Thus, onlytransformed shoots that did not express the coda gene would be expectedto survive this selection step. A total of 141 shoots were harvestedafter selection periods of 10, 20, 30 and 45 days on 5-FC, and PCRanalyzed to determine whether the shoots carried integrated T-DNAs stillharboring the transposon at its original resident position or whetherthey carried the transposon integrated into plant DNA (Table 2). Thefollowing primer sets were used for this purpose:

(1) indicative for the presence of the transposon: (NPTII) (SEQ ID NO:141): AGGAAGGAATTCCCCCGGATCAGC (SEQ ID NO: 142): AGGAGCAAGGTGAGATGACAGG

(2) indicative for the presence of the T-DNA: (CodA) (SEQ ID NO: 143):GAATCAGCTAATCAGGGAGTGTG (SEQ ID NO: 144): GCCATGCGCGTTGTTTCACATCG

(3) indicative for the presence of a T-DNA carrying a non-excisedtransposon (the “full donor site”): 637 bp for F1-R1; 848 bp for F1-R2)P1A: (SEQ ID NO: 145) GCATGCTAAGTGATCCAGATG (F1) P1B: (SEQ ID NO: 146)CTGCAGTCATCCCGAATTAG (R1)

P1A and P1B amplify the upstream “full donor site”, representing thejunction between T-DNA and 5′-transposon end, (651 bp) and P2A: (SEQ IDNO: 147) GGAATTCGCGTAGACTTATATGGC (F2) P2B: (SEQ ID NO: 148)TGATGACCAAAATCTTGTCATCCTC (R2)

P2A and P2B amplify the downstream “full donor site”, representing thejunction between 3′-transposon and T-DNA.

(4) indicative for the presence of a T-DNA that lost the transposon dueto excision (the “empty donor site”, 656 bp): P3A: (SEQ ID NO: 149)GCATGCTAAGTGATCCAGATG (F1) P3B: (SEQ ID NO: 150)TGATGACCAAAATCTTGTCATCCTC (R2)

Twenty-four plants contained both a full and empty donor site,indicating that the transposon in these plants excised from a stablyintegrated T-DNA. These plants were not considered for further studies.

In contrast, thirteen contained the transposon and lacked a full donorsite. DNA gel blot analysis of these plants demonstrated that eleven ofthem contained the nptII gene and lacked the codA gene, indicating thatthey did not contain a stably integrated T-DNA. As shown in Table 2,most of these eleven plants were obtained from the 30-day 5-FC selectionexperiment.

Eight of eleven plants that lacked any T-DNA or backbone DNA sequencescontained a single transposon insert. Because tobacco transformationresults, on average, in the integration of two T-DNAs most of whichstill linked to backbone DNA, the frequency of single-copy andbackbone-free transgenic plants is higher for TDTB transformation.

To confirm the integration of excised transposons into plant genomes, wedetermined the sequence of transposon-plant DNA junctions. Upstreamjunctions were isolated by (i) digesting DNA of the transgenic lines,(ii) circularizing this DNA using T4 DNA ligase, (iii) employing theresulting DNAs as template for a first PCR using the primer pair TR1 andTD1 (SEQ ID NOs: 151 and 152), and (iv) using the resulting templatewith the primer pair TR2 and TD2 for a second PCR (SEQ ID NOs: 153 and154).

Similarly, the primer pair RTR1 and RTD1 (SEQ ID NOs: 155 and 156) wasused for first round amplifications of the downstream junction, and theresulting template was used with RTR2 and RTD2 for second roundamplifications (SEQ ID NOs: 157 and 158).

Sequence analysis of the junction fragments confirmed that thetransposon had in each case excised from the non-integrating T-DNA andintegrated into a unique position in plant DNA. As expected, theintegrated transposons were flanked by eight-base pair direct repeats,created by duplication of the eight-base pair integration site.

Instead of T-DNAs, it is also possible to use plasmids that can bemaintained in Agrobacterium and/or Rhizobium and contain at least onecleavage site. Instead of the transposon ends employed here, it is alsopossible to use the termini of other transposable elements that arefunctional in plants.

EXAMPLE 8 Enhanced Fidelity of DNA Transfer with Plasmids Carrying thevirC Operon

To study whether virC genes influence the frequency and fidelity of theT-DNA transfer, we isolated the entire virC operon (SEQ ID NO. 167) fromAgrobacterium via PCR approach using virC operon specific primers (SEQID NO. 168) 5′ GTTTAAACAGCTTCCTCCATAGAAGACGG 3′ and (SEQ ID NO. 169) 5′TTAATTAATCGTACGGGGGTGTGATGG 3′.

The PCR amplified virC operon was cloned into PmeI-PacI sites of thepSIM1008 plasmid DNA backbone that contains Le01 as initial cleavagesite and the conventional Left Border of pTiC58 for secondary cleavage.Stably transgenic tobacco plants produced with the resulting plasmidpSIM1026 were analyzed, and the data were compared with those obtainedwith plasmid pSIM1008. Table 3 shows that the presence of the virCoperon increased the frequency of backbone-free transformation more thantwo-fold. TABLE 1 Backbone-free Transformation with transformation withtransfer DNA still linked Plasmid transfer DNA to backbone Benchmarkvector 39% 61% Control vector 26% 74% pSIM794 55% 45% pSIM795 44% 56%

TABLE 2 Carrying at least one T-DNA Number of Only carrying comprisingthe transformed the transposon transposon at its Treatment plants inplant DNA original position 10 days on 5-FC 39  0 (0%)   4 (10%) 20 dayson 5-FC 51  3 (6%)  12 (24%) 30 days on 5-FC 35  9 (26%)  5 (14%) 45days on 5-FC 16  1 (6%)   3 (19%) Total 141 13 (9%)  24 (17%)

TABLE 3 Genotypes of transgenic tobacco plants produced with pSIM1026and pSIM1008 Integration of Integration of sequences comprisingsequences both the actual Integration of between transfer DNA plasmidbackbone Leo1 and Left and plasmid backbone sequences Plasmid Borderonly (1) sequences (2) only (3) pSIM1008 16.9 ± 1.7 67.7 ± 5.3 21.7 ±3.7  pSIM1026 39.5 ± 4.1 51.5 ± 0.8 9.2 ± 3.4

(1) Visualized using primers 5′ TGCTCCTGCCGAGAAAGTAT 3′ (SEQ ID NO: 170)and 5′ AGCCAACGCTATGTCCTGAT 3′ (SEQ ID NO: 171)(2) Visualized using primers SEQ ID 170 and SEQ ID 171, SEQ ID 172 andSEQ ID 183

(3) Visualized using primers 5′ GAATCAGCTAATCAGGGAG 3′ (SEQ ID NO: 172)and 5′ GCCATGCGCGTTGTTTCACATCG 3′. (SEQ ID NO: 183)

SEQUENCE TABLE SEQ ID NO: NAME (if any) SEQUENCE 1 Rb01GTTTACCCGCCAATATATCCTGTCA 2 Rb02 AATTACAACGGTATATATCCTGCCA 3 Rb03CATGACAGGAACATATATCCTGTCA 4 Rb04 AATTACAACGGTATATATCCTGTCA 5 Rb05CCTGACCACAAGATATATCCTGTCA 6 Rb06 CTAGACAAGGGGATATATCCTGTCA 7 Rb07CATTACTTTAGAATATATCCTGTCA 8 Sy01 CTTTACACAACAATATATCCTGTCA 9 Sy02GTCTACACAACAATATATCCTGTCA 10 Sy03 GTTTAAACAACAATATATCCTGTCA 11 Sy04GTTTACACAACAAGATATCCTGTCA 12 Sy05 GTTTACTCAACAATATATCCTGTCA 13 Sy06GTTAACACAACAATATATCCTGTCA 14 Sy07 GTTTACACAACACTATATCCTGTCA 15 Sy08GTTTACACAACAATATATCCTGGCA 16 Sy09 GTTTACACAACAATAAATCCTGTCA 17 Sy10GTTTACACAACAATATGTCCTGTCA 18 Sy11 GTTTACACAACAATATATGCTGTCA 19 Sy12GTTTACACAACAATATATCGTGTCA 20 Sy13 GTTTACACAACAATATATCCAGTCA 21 extendedUI ACGAACGGATAAACCTTTTCACGCCCTTTTAAATATCCGTT region ofATTCTAATAAACGCTCTTTTCTCTTAGAGATCTCAAACAAA PSIM551CATACACAGCGACTTATTCACAACTAG 22 DI region ofGGGCCCGGTACCCGGGGATCAATTCCCGATCTAGTAACATA pSIM551GATGACACCGCGCGCGATAATTTATCCTAGTTTGCGCGCTA TATTTTGTTTTCTATCGCGTATTAAAT 23potato St01 GTTTACATCGGTATATATCCTGCCA 24 primer YGR CAG GAT ATA TNN NNNKGT AAA C 25 anchor primer GAC CAC ACC CGT CCT GTG 26 ArabidopsisGTTGACATCACGATATATCCTGTCA At01 27 CON1 [A/C/G] [A/T] [A/T] [G/T] AC[A/C/T] N [C/G/T] [A/ C/G] [A/C/G] [A/C/G] ATATATCCTG [C/T] CA 28 tomatoLe01 CATTACCAACAAATATATCCTGGCC 29 tomato Le02 CTCTACCTCTGAATATATCCTGCGG30 tomato Le03 GCATACCTCTGAATATATCCTGCGG 31 potato St03GTTTACCTTAGCATATATCCTGCAT 32 alfalfa Ms01 GTATACCTCTGTATACATCCTGCCG 33barley Hv01 ATATACCAAATGATACATCCTGCCC 34 rice Os01ACTTACTCAAGGATATATCCTGGCT 35 rice Os0 CACTACAAAAAAATATATCCTGCAT 36 rice0s03 ATGTACGTATATATATATCCTGTGT 37 wheat Ta01 ATATACGGAGCAATATATCCTGTCC38 Soybean Gm01 AAAAACTGTTTTATATATCCTGTCA 39 Soybean Gm02AATAACTCTGAAATATATCCTGTGT 40 Potato St04, ACCTACCCCAAAATATATCCTGCCT 41tomato Le04 GGAAACTGTCTAATATATCCTGTGA 42 tomato Le05ACCTACCCCAAAATATATCCTGCCC 43 tomato Le06 GTTTAGACTTGTATATATCCTGCCC 44tomato Le07 TCTTAGAACTCAATATATCCTGTAC 45 tomato Le08CGTTAACACTGTATATATCCTGTAA 46 tomato Le09 GAATTATTTTGCATATATCCTGTAA 47tomato Le10 TTGTTCCTGGCCATATATCCTGCCA 48 tomato Le11GGTACCATGTAGATATATCCTGCTT 49 M. truncatula GTATACCTCTGTATACCTCCTGCCGMt01 50 maize Zm01, GCGTACGCATTTATATATCCTGTGG 51 Zm01-derivedGCTTACGCATTTATATATCCTGTGG Zm01M1 52 Brassica rapaCCCTACTGTATAATAAATCCTCTAG Br01 53 tomato Le10 TTGTTCCTGGCCATATATCCTGCCA54 tomato Le1 GGTACCATGTAGATATATCCTGCTT 55 tomato Le12GTTCCGGTTGACATATATCCTGACA 56 tomato Le13 CACTACCGCCTCATAGTTCCTGCCA 57soybean Gm01 TAAAGCAACACCATATATCCTGACA 58 M. truncatulaGATTAGACAAATATTTATCCTGCCA Mt02 59 rice 0s04 CTCTACTACCCGAGATGTCCTGGCA 60potato St05* GTTTGACACGACATATATACTGCAA 61 potato St06*GTTTACCGTGGCACTTATGTGATGA 62 potato St07 CATTACCAACTATTATATCCTGGCC 63tomato Le14 GTTTACTTGAAGATATCACCTATGT 64 tomato Le15TTCCATACGAAGAGAAGTCCTGTCA 65 tomato Le16 TTCTAGCTGCAAATATATCCTGGCT 66tomato Le17 GTTGACATGGATGAATATCCTGTCA 67 tomato Le18GTTCAGCTTAGCATATATCCTGCAT 68 tomato Le19 TTCCAGAAGTAGATATATCCTGTTG 69tomato Le20 TGATTGCATCAAATATATCCTGCCA 70 tomato Le21ATCCCCACCCATTTATATCCTGCCA 71 tomato Le22 CATCCCCACCATTTATATCCTGCCA 72tomato Le23 GTCAGGAAGTGAATATATCCTGACA 73 tomato Le24GTTTAAACCAATATATATCCTGATT 74 tomato Le25 AGTTATAAACTTATATATCCTGTTG 75tomato Le26 CTAAAGTTGTACATAAATCCTGTCT 76 tomato Le27TTCTACACAAAGACAAATCCTGGCG 77 tomato Le28 ATTAACAACGTTAGAAGTCCTGGCG 78 M.truncatula CATGACCCTGCAATATGTCCTGTGG Mt03 79 maize Zm02AACTTAAAGATAAGAAGTCCTGCCA 80 oat As01 CTGTACAATAGGACAAATCCTGTCG 81potato St08* TTTTACCCGTGATATATCCCAGCC 82 tomato Le29GATTGCATCAAATATATCCTGCCA 83 tomato Le30 AAGTACCGATGATATATCCTGCGT 84 CON2[A/C/G] - [A/C/T] - [A/C/T] - [G/T] -A- [C/G] - NNNNNN-A- [G/T] -A-[A/C/T] - [A/G] -TCCTG- [C/G/T] - [A/C/G] -N 85 Ca01CATTACCAACAAATATATCCTGGCC 86 St02 CATTACCAACAAATATATCCTGGCC 87 UI regionCTTAGAGATCTCAAACAAACATACACAGCGACTTATTCACA ACTAGTC 88 overdriveCAAACAAACATACACAGCGACTTA 89 UI-derivedTTAGAGATCTCAAACAAACATACACAGCGACTTATTCACAA CTAGTAC 90 UI-derivedAGAGATCTCAAACAAACATACACAGCGACTTATTCACAACT AGTCAAC 91 UI-like fromAGAAACAATCAAACAAACATACACAGCGACTTATTCACACG Agrobacterium AGCTCAA 92UI-like from GCCCTTTTAAATATCCGATTATTCTAATAAACGCTCTTTTC AgrobacteriumTCTTAGG 93 UI-like from TGACGAACTGACGAACTGACGAACTGACGAACTGACGAACTAgrobacterium GACGAAC 94 UI-like fromTAACAATTGAACAATTGAACAATTGAACAATTGAACAATTG Agrobacterium AACAAAC 95UI-like from TAGACATTGCACATCCAAAGGCAGGCACGTACAAACGAATT AgrobacteriumTATTTAG 96 UI-like from GAAGGCACGAAGGCACGAAGGCACGAAGGCACGAAGGCACGAgrobacterium AAGGCAC 97 UI-like fromTCATCACCGCCGTCCTAAACAAACATACCTCCACACAAATT Agrobacterium TATCTAC 98UI-like from AGATCTCAAACAAACATACACAGCGACTTATTCACAACTAG AgrobacteriumTACCAAC 99 UI region TGACGAACTGACGAACTGACGAACTGACGAACTGACGAI4CT ACCAAAC100 UI-derived CTGACGAACTGACGAACTGACGAACTGACGAACTGACGAAC TACCAAC 101UI-like TGTCTTTATCTCTTGTTGCCAAAACTGCTCTCGAGTCGAGT CACCAAC 102 DownstreamGTCAGCATCATCACACCAAAAGTTAGGCCCGAATAGTTTGA from right AATTAGAAA border103 Downstream AACACTGATAGTTTAAACCGAAGGCGGGAAACGACAATCTG from rightATCATGAGCGG border 104 DownstreamAATAACAATCTCATGTTAGGTAATAATATCACCCAATCAAC from right GCGGCCA border 105Downstream GCACTAATATAAGAAATGTCCTGTCAGCACTAATATAAGAA from right ATGTCborder 106 Downstream AACCTATTCGTTAATAGGGACGTCGTACCTACTTCCCTTCC fromright AGCGCAGCA border 107 DR domain [A/C/T] - [A/C] - [A/C/T] -[A/G/T] - [A/T] -T- [A/C] -G- [G/T] - [G/T] 108 DI regionGAGGTATAGAGGCATGACTGGCATGATCACTAAATTGATGC from potatoCCACAGAGGAGACTTATAACCT 109 DI regionGGGCCCGGTACCCGGGGATCAATTCCCGATCTAGTAACATA from potato GATGAC 110DI-region GGGCCCGGTTCCCGGGGATCAATTGGGCCCGGTACCCGGGGATCAATTCCCGATCTAGTAACATAGATGAC 111 DI-regionGGGCCCGGTACCCGGAGGAGACTCCGATCTACGGCGCCAAA TTCAAG 112 DI-regionCTGAGGACATTCAGAAGATTGGTTATATCCTCTTTCAAGAC GCTAAGCAA 113 DI-regionGAGGTATAGAGGCATGTCTGGCGTGATCACTAAATTGATGC from potatoCCGCAGAGGGGACTTATAACAT 114 DI-regionGGGGCCCGGTACCCGTTAGGGCTAGCCCGAAAGGGCCGCGG from alfalfa GCAGCCC 115repeat CCCG 116 AF region TCTCCATATTGACCATCATACTCATTGCTGATCCATGTAGATTTCCCGGACATGAAGCCATTTACAATTGAATATATCCTGC CGCCGCTGCCGCTTTGCACCC 117 AFregion TGAATTCAGTACATTAAAAACGTCCGCAATGTGTTATTAAGTTGTCTAAGCGTCAATTTGTTTACACCACAATATATCCTGC CACCAGCCAGCCAACAGCTCCCCGACC118 AF region ATCTGGTAATATAGCAAAAACGTGCTCAAAAATCGCTTCAAAGCTCTTGTACTTAGCTCGTTTACACCACAATATATCCTGC CACCCC 119 AF regionTACATTTTATATTCGATAAAGCATGCGTTAAAACGACTTCGCATGTCCATATCTAATCTGTTTACATCACAATATATCCTGC CACCCAAGGAGCGACGCCTTCTGGCC 120UL domain A [C/T] T [C/G] A [A/T] T [G/T] [C/T] [G/T] [C/G] A [C/T][C/T] [A/T] 121 left border [A/G] TTTACA [A/C/T] [A/C/T] [A/C/T]consensus [C/G] AATATATCCTGCC [A/G] 122 CCN(1-11) CCN(1-11) CCN(1-11) CC123 AF region AAATCTGATTGATAAAGGATCGATCCTCTAGAGTCGACCTGCAGTACTTACGTACAATTGTTTACACCACAATATATCCTGCCACCGGATATATTGCCTAGGAGCCAGCCAACAGCTCCCCGA CC 124 AF regionAAATCTGATTGATAAAGGATCGATCCTCTAGAGTCGACCTGCAGTACTTACGTACAATTGTTTACACCACAATATATCCTGCCACCCCTAGGAGCCAGCCAACAGCTCCCCGACC 125 AF regionGTTTACACCACAATATATCCTGCCACCCCTAGGAGCCAGCC AACAGCTCCCCGACC 126 AF regionGTAAAAAATAAAAGTGAAAATTCAATGAATTAACACAAATATAAATGTAATATAAAATTGTATACCTCTGTATACATCCTGCCGCCAAGCTTCCAGCCACCTAGGAGCCAGCCAACAGCTCCC CGACC 127 AF regionAATGGAGGTAAGTGTTTCTGCTCAGTGCTGATAGATGTAAATATCTCTGTTATGAAGCCGTATACCTCTGTATACATCCTGCCGGGATGTATACCCTAGGCCAGCCAGCCAACAGCTCCCCGA CC 128 AF regionTGTTGAAGGCTTGGATGTGATTAAGAAGGCCGAGGCTGTTGGATCTAGTTCTTGAAGTTCATTACCAACAAATATATCCTGGCCCCCCTAGGAGCCAGCCAACAGCTCCCCGACC 129 IHF site [A/T] ATCAANNNN [A/G] 130search motif CAGGATATATNNNNNNGTA 131 extended DNAGGCTGCACTGAACGTCAGAAGCCGACTGCACTATAGCAGCG region ofGAGGGGTTGGATCAAAGTACTTTGATCCCGAGGGGAACCCT pSIM843B forGTGGTTGGCATGCACATACAAATGGACGAACGGATAAACCT initialTTTCACGCCCTTTTAAATATCCGATTATTCTAATAAACGCT cleavageCTTTTCTCTTAGAGATCTCAAACAAACATACACAGCGACTTATTCACAACTAGTGTATACCTCTGTATACATCCTGCCGGGGCCCGGTACCCGTTAGGGCTAGCCCGAAAGGGCCGCGGGCAG CCCGTTAGCCCGCATAACTGCAGCCCGGG132 extended DNA CAGTACTTACGTACATAACAAAAAAAAATTCTATAAATTAT region ofATATATTTTTCAAATAATTCTTTACACAGTTGATTATCAAA pSIM843B forGTAAAAAATAAAAGTGAAAATTCAATGAATTAACACAAATA finalTAAATGTAATATAAAATTGTATACCTCTGTATACATCCTGC cleavageCGCCAAGCTTCCAGCCACCTAGGAGCCAGCCAACAGCTCCCCGACCGGCAGCTCGGCACAAAATCACCACTCGATACAGGCAGCCCATCAGTCCGGGACGGCGTCAGCGGGAGAGCCGTTGTAAGGCGGCAGACTTTGCTCATGTTACCGATGCTATTCGGAAG AACGGCAACTAAGCTGCCGGGTTTGA 133alternative CCCGAAAAACGGGACAGGATGTGCAATTGTAATACCGTCAC finalACGCGACGCTATTACAATTGCCATCTGGTCAGGGCTTCGCC cleavage site CCGACACCCC 134alternative CCCGAAAAACGGGACAGGATGTGCAATTGTAATACCGTCAC finalACGCGACGCTATTACAATTGCCA cleavage site 135 alternativeCCCGAAAAACGGGACAGGATGTGCAATTGTAATACCGTCAC final ACGCGACGCTA cleavagesite 136 alternative AAAACGGGACAGGATGTGCAATTGTAATACCGTCACACGCG finalACGCTATTACAATTGCCATCTGGTCAGGGCTTCGCCCCGAC cleavage site ACCC 137alternative ACCGAAAAACGGGACAGGATGTGCAATTGTAATACCGTCAC finalACGCGACGCTATTACAATTGCCATCTGGTCAGGGCTTCGCC cleavage site CCGACACCCC 138Ac ATGACGCCTCCGGTTGGAAATAATCCTCCCTCAGGCTCAGC transposaseCATAAGATTGGCCAAGTTGATGTCTACCACAAGAGCGCCTT geneCTACTCGCAAAACAAATTCCGTATTCTCTGCATATGCTCAAGGTATATATTAGAAAAACAGTAGCAATAGCATTAGCATTACTAATTGGTTGTAGATTGGGAAGCATCATATTGACTGTAGAATAATACGAAAAATCTGTTTATAACAGGGTTGAAAAGAAAAGCTGAAGCCTCTTCTAGTCGGATTCAGAATGTACGTGCACGTGCGCGTGGGCATGGATGTGGCCGCACATCACCATCATCATCAACAGCTGAGGCCGAGAGGCATTTTATTCAGAGTGTAAGCAGTAGTAATGCAAATGGTACAGCTACAGATCCGAGTCAAGATGATATGGCTATTGTTCATGAACCACAACCACAACCACAACCACAACCAGAACCACAACCACAGCCACAACCTGAACCCGAAGAAGAAGCACCACAGAAGAGGGCAAAGAAGTGCACATCGGATGTATGGCAGCATTTCACCAAGAAGGAAATTGAAGTGGAGGTCGATGGAAAGAAATACGTTCAGGTATGGGGACATTGCAACTTTCCTAATTGCAAGGCTAAGTATAGGGCTGAGGGTCATCATGGAACAAGCGGATTTCGAAATCACTTGAGAACATCACATAGTTTAGTTAAAGGTCAGTTGTGTCTAAAAAGTGAAAAGGATCATGGCAAAGACATAAATCTCATTGAGCCTTATAAGTACGATGAAGTGGTTAGCCTAAAGAAGCTTCATTTGGCAATAATCATGCATGAATATCCTTTCAATATTGTAGAACATGAGTACTTTGTTGAGTTTGTTAAGTCTCTGCGCCCTCACTTTCCAATAAAGTCCCGTGTCACTGCTAGAAAATATATCATGGATTTGTATTTGGAAGAAAAAGAAAAGTTGTATGGAAAACTAAAAGATGTTCAGTCTCGCTTCAGTACAACTATGGATATGTGGACATCTTG 139 5′ transposonCAGGGATGAAAGTAGGATGGGAAAATCCCGTACCGACCGTT endATCGTATAACCGATTTTGTTAGTTTTATCCCGATCGATTTCGAACCCGAGGTAAAAAACGAAAACGGAACGGAAACGGGATATACAAAACGGTAAACGGAAACGGAAACGGTAGAGCTAGTTTCCCGACCGTTTCACCGGGATCCCGTTTTTAATCGGGATGATCCCGTTTCGTTACCGTATTTTCTAATTCGGGATGACTGCA 140 3′ transposonGTAGACTTATATGGCTTCTTATGTTAGCCAAGAGCCCAAGA endCTTATCACTTATGTGCTACATTAAACTATGTGTGCTCCAGATTTATATGGATTTTATCTATGTTTAATTAAGACTTGTGTTTACAATTTTTTATATTTGTTTTTAAGTTTTGAATATATGTTTTCATGTGTGATTTTACCGAACAAAAATACCGGTTCCCGTCCGATTTCGACTTTAACCCGACCGGATCGTATCGGTTTTCGATTACCGTATTTATCCCGTTCGTTTTCGTTACCGGTATATCCCGTTTTCGTTTCCGTCCCGCAAGTTAAATATGAAAATGAAAACGGTAGAGGTATTTTACCGACCGTTACCGACCGTTTTCATC CCTA 141 NPTII primerAGGAAGGAATTCCCCCGGATCAGC 142 NPTII primer AGGAGCAAGGTGAGATGACAGG 143codA primer GAATCAGCTAATCAGGGAGTGTG 144 codA primerGCCATGCGCGTTGTTTCACATCG 145 P1A primer GCATGCTAAGTGATCCAGATG 146 P1Bprimer CTGCAGTCATCCCGAATTAG 147 P2A primer GGAATTCGCGTAGACTTATATGGC 148P2B primer TGATGACCAAAATCTTGTCATCCTC 149 P3A primerGCATGCTAAGTGATCCAGATG 150 P3B primer TGATGACCAAAATCTTGTCATCCTC 151 TR1primer ATCGGTTATACGATAACGGTCGGTACG 152 TD1 primerACGAAAACGGAACGGAAACGGGATATAC 153 TR2 primer GATTTTCCCATCCTACTTTCATCCCTG154 TD2 primer GTAGAGCTAGTTTCCCGACCGTTTCAC 155 RTR1 primerGCACATAAGTGATAAGTCTTGGGCTC 156 RTD1 primer CGACCGGATCGTATCGGTTTTCGATTAC157 RTR2 primer CTAACATAAGAAGCCATATAAGTCTAC 158 RTD2 primerCGGTAGAGGTATTTTACCGACCGTTAC 159 upstreamATAGATAAGAGGAGTTTGTTACAAATTTCTACTCCACATTG junction ofATGAGAAATATACTAATGTTATCTCCCCTTCCCTCTATTAG plant 1TAGATCTTACTCTATGTTAAAACATGACAAGAAATAGAGAGAGAACTCACACTTTCTTCCTCATCTGCTACTTCTGGTGCCGAAGAAGTTTTACTCAAAGAGTCTAATTTAAGGCAACGAAGCATGTCCTTTTGTCTCTTGCAAGTATTGCAAGAAGGCAGGACACACTTTAAAGAAGTGTTATAAGTCATCCATTTTCCTCTGTCTTCAATTTCTTAAAGACCAAAAGATCCAGTCTTTTGTGTCCATGTTGATAATTTTACTCTAATACTCTTAGCTTCCA 160 downstreamAGCTTCCACATCCCAATTTGGTGATCATTCAGCACATAAAT junction ofTTGCTCAGAAGCAATAGGAATATCTCATGTCTCTTCCTTCC plant 1AAATAATCAATTCTCACCTAGGTTCAATAATGATGTTTCTTTTAGAGAGATTTCTGACTATGATCATTTTGCAGGTTTAATTAGTACATTTTTTGTAGTTAATTATGTGTTTTTTCATGCATGTTCATCATTGCAATTAGGGGTAGATACTTGAATCTTTTACTTGGGCCACTAGCCACATGACTCCATTTATGGTGTTTATAAGCTATATCAGTGTATATCACATTGTATTTCCATATATCTCAGGTGTACCATATATATCTGTGATTATGTGAAAGACCCCCCTAATTTGTGTCAAGACTGACAATGCTCTGTCAATCAGTGTAGCAAAATAAAAATAAAATAAAATCAAGGATTAGTACAACACCATCCAGGAACCTTTACTAGAAAATTAGTATACCATATGAGTCTTTTACAGTTTGGATCTATCATGGAGTAAAAGAATACATTGCAGATTAGGATTATTCAAAATATGCCTTCTTGCAATCTAC GTTGTGATCAACAGATATA 161upstream ATTCTCACCAAAAATTGAGCTGATTAGATAAAAAAAGATCA junction ofATTTGTTAAGACCAGCAGCAGCTCTTCAGTACCATTTCATG plant 2TCTTAACAGGACATATATATATATATATAGATATAGAGAGAGAAAGTGGGCAAGACTTGATTTTTATAGATCTAGAGAGAGA AAAGGAGAGTTGGG 162 downstreamGAGTTGGGGAGAAAAAGAAGGGATTTTTACAGATCTAGAGA junction ofGAGAAAGACTTGATTCTTCCTATTTTCTCTTCACCATTTCC plant 2TATGTTTTCTCTCCCTCTCTTTTCTCTTTCTTGATTTCTCTATAAATTTTCACTCATTAGTATATTCATCACTCTCAATTTACCTTTTATATAAAAATAAAAACAATAAAAATTACTAAATACATTTAATTTTAATTATAAATAGAAATTATTACACTATTGATTTTTTATTTGACTTATTTATTTATTTTAGTCTATTCGAAAAATATGTCTTTTTCGTTTTCTAATAACTCTTTCATTTTAGTCTTTTCCATTTAATATTACAAAATTTAAAAAAATGCATTTTGGTACCTTTTTAAGATTACAAAATTTGAATATATTATTTACTTTATTAAATTACGCATTTAATCAAAACAAAACAATCAAAATGAAAGCATTTTGGTACCTTCTAGAATACGTATATTTAATTTGAAATTACAAAATTTGAATATATTCTTTATTTTGTTAAATTACGTATTTAGTCAAAACAGGACAATAAAAAAAAACGAAAGGAGTAATTACTAATACAATAACATTTTGACTAAAATTAAAATTAAAGAAAAAAAGGATTTTGGTACCTTCTAG 163 upstreamTGTGATTTAGGAAGGTAAGATGACTTTGCAAGGATTGTCTT junction ofCAAATGGCATAAATCTAACATTCAAAATTAAGTCTATTTTT plant 3AAACAATAAAAATACATGAGATTTGCAATTTATAAGTCAACGTTGTCATATAACCCATTAGTTCGGTTTTAAGGATATGAATAGAGGTTTGAAACGTGTTGCAAATGCTCTCAACTATGGACATAACCCAGTACCCATGTCAGCACTAAGGACCACCGGGAAACACCCCCCGGAACCATCGGAACCACCAGATACCACTAGCTACATGATGGAGGACCCAGAATCGAATCAGAGCTTTAAGGATATTCTCCTGAACAAAAATAAGGAGATAAATCAACTACACCACC CTACCGGAAC 164 downstreamACCGGAACTGGAACAGCAGGATCATACAGAGGACCTTGACA junction ofTGGACTCCATCCAACTATCGACAGAGGACAAGCAACAAATT plant 4TACCAACCGTGGAACCTCTCTGTGATAGTAAAGGTATTTGGAAAAAAATCGCCCACGCATACTTGAAAAACAAGTTGGTTGATCTATGGAAGCGATCAGAACCTCTAACACTGATAGATTTTGGCTGTGAATACTTTATATTGCAAAATTCAATAATCCAACCAGCCTACATAAGTCCCTCCATGAGGGTCCGTGGTTCATCGCAGGAAACTTCCTGTTAGTAAAAAAAATGGGAGCCAAACTTTGTGCCAGACACATCAACACTCACCCATACAACGATATGGGCAAGGCTGCTGCAACTCCCAGCGGAGTTCTATGACAGGCAAATACTAGAAAAGGTAGGGGGAAAGCTCGGGTCCCTCCTAAAAATTGATACCTGCACCTCTGCTGCACTAAGAGGACGTTATGCACGCATACAGGTTCAGCTAGAGAATCCAGTCAAGACGACGGTCAAAATTGGAAACCATGTTCAAAAAGTGGTATACGAGGGGGACAAAATCCTTTGCACAGAATGTGGGAGACTCGGGAACACCTTATTGACCTCATCCAGGATTTTGAGATGATGGGTACACGATTATAAAAAAGTTGATCTATGATTTAAATTTGATCGGTTTAATATTTAAATTTTTACTACTAAAAACCGTTAAATTTTTAAAATTATAGGTCTAAAATTAATTCTTATATATATATATATACACACACCAATTACCACTTAGAGAAGTGTTATCTAATTTTAGAAAGAAAAATAAAACAAGATAAATATAAATTTCAAATTTCTAACCTCGTGGAGAGAGGTGCACCCAGTCATAATCGCATTATG TGATACTTCAAGTG 165 upstreamAGATCGAGTGAGAAGTAGCTGGAAACATCATGAGTGGCAG junction of plant 4 166downstream AGTGGCAGAAGTGGAAGAGATAAAACTCATGATGATTGTAA junction ofTGAGGGTGGTGGACAAGATGAATCTGGTGCCCAAAACAACA plant 4AAAATACTAATGCCAACAAAAGATCAGGACCAACGGTGCCACCTAAAAGGGGAAGCATAGCAAAACAGATAGTACGAGATTTAAAGGATACATCAAGCTCTCTGAGTACTGTATTCACATTGTTTTTCTTTAACTTCCTTCTCATGGCGATTATATCGACAAATTATGAGAACAAAATATAGGAAGTTTACAACATTGAGGAAAGCAAGTAACCAGTAGTAATAATCTAAATGACCATTGTTAATATTACTTGACAACCAGCTAACTCCACCTCCATATGAAGTAACACTATCCACAACATTCACTAAAACACTCCCAAAAAAGCCAGCTACAGACATTCCAAGTGTGAAAATAGCCACAACAAAACTAGACATGCTTTTTGGAAGTTCAGAGTAAAGGAACTCTACCAATCCGATTGCATTGAAAGCATCAGCTAGTCCAAGAAGCACGTACTGTGGCACGAACCACATAGCCGACATGTTTATATTTAGACTGTCTTGTGGATCTTTCTGATCAATTGCTATGCCCCGCCTTATGCCTTCTGTTATCGCTGAAAGTACCATCG 167 virC2 regionTTAACTCCGCTCGATATCGATGAAGCATTGTCGACCTACCGCTATGTCATTGAACTGCTGCTGAGCGAGAACTTGGCAATTCCGACAGCCGTATTGCGCCAACGCGTGCCGGTTGGTCGATTGACCACATCGCAGCGCGCGATGTCGGACATGCTCGCAAGCCTTCCAGTTGTACAGTCTCCCATGCACGAGAGAGACGCATTTGCCGCGATGAAGGAACGTGGCATGTTGCATCTCACATTGCTGAATATGAGAACCGATCCGACAATGCGCCTCCTCGAGCGGAATCTCAGAATCGCCATGGAGGAACTCGTCACTATCTCCAAATTGGTTAGCGAAGCCTTGGAGGGGTGAAGATGGGAATTCGCAAACCCGCTTTGTCTGTCGGGGAGGCCAGGCGGCTTGCCGCCGCTCGACCCGAAATCGTCCATCCTTCTTTGCCTGTTGCCACCCAAAACTCGACCCTGCCGCAGCCGCCTGAAAATCTCGACGAGGAAGATCGACGACCTGCCCCAGCCACCGCCAAGCGTTGTCACAGCTCTGATCAGCAATCGATGCTGACCGTGGATGCTTTGAGTTCGACGACAGCGCCAGAAAGGATCCAGGTCTTCCTTTCAGCGCGCCCGCCCGCGCCTGAAGTATCGAAGATATATGACAACCTGATCCTGCAATACAGTCCTTCCAAGTCGCTACAAATGATCTTGCGCCGTGCGCTTGGCGATTTTGAAAACATGCTGGCGGATGGATCGTTTCGTGCGGCTCCGAAGAGTTATCCGATCCCTCACACAGCTTTCGAAAAATCAATCATCGTTCAGACCTCCCGCATGTTCCCGGTCTCGCTAATAGAAGCCGCTCGCAATCACTTTGATCCATTGGGATTGGAGACCGCCCGGGCTTTCGGCCACAAGCTGGCTACCGCAGCGCTTGCATGTTTCTTTGCTCGGGAGAAGGCAACGAACAGCTGATCTCTCAAAAGATAGGACCCATCCAATCACTCCGCAGTGCTGAGTTTTTCGGATAGTACCGAGGAAAGGCAGCTTTGCCAAGCCGCATAGCAATCTGCTCACGTTGGGAACAGATTGCTAAAGGCGAAATGCACCTCTACCT CAGGCCGCCATCACACCCCCGTACGA 168virC primer GTTTAAACAGCTTCCTCCATAGAAGACGG 169 virC primerTTAATTAATCGTACGGGGGTGTGATGG 170 primer TGCTCCTGCCGAGAAAGTAT 171 primerAGCCAACGCTATGTCCTGAT 172 primer GAATCAGCTAATCAGGGAG 173 humanTGGCAGGATATATACATATGTACAC AC027708 174 human CTGCAGGATATATTTCTCAGTAAACAC024192 175 human TGCCAGGATATATACATGGCTAATG AC003685 176 humanGGCCAGGATATATTACCCAGTAATT AL390883 177 human AGGCAGGACTTCTGTGTATGTTAACAC022858 178 mouse AGGCAGGACTTAATGTGGTGTAAAC AC110541 179 mouseTGGCAGGATATATATCTTGGTAAAT AC132685 180 rat AC096051TGGCAGGATATATGGCATTGTCATT 181 Neurospora ATACAGGATATATAGGTAGGTAAAGBX897673 182 Saccharomyces AGACAGGATATATTGGAAGGTATTC AJ316068 183 primerGCCATGCGCGTTGTTTCACATCG 184 UF region ofTCCTTCATAGCTACACTTTCTAAAGGTACGATAGATTTTGG pSIM108 ATCAACCACACACACTTC 185UF region of GTAAAAAATAAAAGTGAAAATTCAATGAATTAACACAAATA pSIM843BTAAATGTAATATAAAATT 186 UF regionTGTTGAAGGCTTGGATGTGATTAAGAAGGCCGAGGCTGTTG ofpSIM781 GATCTAGTTCTTGAAGTT187 C-clusters of CCACAATATATCCTGCCACCGGATATATTGCCTAGGAGCCA PSIM831GCCAACAGCTCCCCGACC 188 C-clusters ofCCTCTGTATACATCCTGCCGCCAAGCTTCCAGCCACCTAGG pSIM843AGCCAGCCAACAGCTCCCCGACC 189 modified CCCTACTGTATAATAAATCCTGTAG Brassicarapa cleavage site Br01M1 190 modified CTCTACTGTATAATAAATCCTGTCGBrassica rapa cleavage site BrM2 191 approximate CCCGAAAAACGGGA part ofalternative final cleavage site that is transferred to plant cell 192Arabidopsis ACCGAAAAACGGGA sequence resembling SEQ ID 191 193 Maize Zm03GCGTACGCATTTATATATCCTGTGG 194 Zm03-modified GCTTACGCATTTATATATCCTGTGGcleavage site Zm03M1 195 Gm01-derived AAATACTGTTTTATATATCCTGTCA GM01M1196 Gm02-derived AATTACTCTGAAATATATCCTGTGT GM02M1 197 Brassica rapaTGGAACTGTTCTATATGTCCTGTCA Br02 198 Br02-derivedAGGAACTGTTCTATATGTCCTGTCA Br02M1 199 UI region ofCTTAGAGATCTCAAACAAACATACACAGCGACTTATTCACA SEQ ID: 87 ACTAGTC 200 UI-likeAGAAACAATCAAACAAACATACACAGCGACTTATTCACACG region of AGCTCAA SEQ ID: 91201 UI-like GCCCTTTTAAATATCCGATTATTCTAATAAACGCTCTTTTC region of TCTTAGGSEQ ID: 92 202 UI-like TGACGAACTGACGAACTGACGAACTGACGAACTGACGAACT regionof GACGAAC SEQ ID: 93 203 UI-likeTAACAATTGAACAATTGAACAATTGAACAATTGAACAATTG region of AACAAAC SEQ ID: 94204 UI-like TAGACATTGCACATCCAAAGGCAGGCACGTACAAACGAATT region of TATTTAGSEQ ID: 95 205 UI-like GAAGGCACGAAGGCACGAAGGCACGAAGGCACGAAGGCACG regionof AAGGCAC SEQ ID: 96 206 UI-likeTCATCACCGCCGTCCTAAACAAACATACCTCCACACAAATT region of TATCTAC SEQ ID: 97207 UI region of AGATCTCAAACAAACATACACAGCGACTTATTCACAACTAG SEQ ID: 98TACCAAC 208 UI region of TGACGAACTGACGAACTGACGAACTGACGAACTGACGAACT SEQID: 99 ACCAAAC 209 UI region ofCTGACGAACTGACGAACTGACGAACTGACGAACTGACGAAC SEQ ID: 100 TACCAAC 210 UIregion of TGTCTTTATCTCTTGTTGCCAAAACTGCTCTCGAGTCGAGT SEQ ID: 101 CACCAAC211 UF-like region of TCTCCATATTGACCATCATACTCATTGCTGATCCATGTAGA SEQ ID116 TTTCCCGGACATGAAGCC 212 UF-Iike region ofTGAATTCAGTACATTAAAAACGTCCGCAATGTGTTATTAAG SEQ ID 117 TTGTCTAAGCGTCAATTT213 UF-like region of ATCTGGTAATATAGCAAAAACGTGCTCAAAAATCGCTTCAA SEQ ID118 AGCTCTTGTACTTAGCTC 214 UF-Iike region ofTACATTTTATATTCGATAAAGCATGCGTTAAAACGACTTCG SEQ ID 119 CATGTCCATATCTAATCT215 AF-like region of CCTGCCGCCGCTGCCGCTTTGCACCC SEQ ID 116 216 AF-likeregion of CCTGCCACCAGCCAGCCAACAGCTCCCCGACC SEQ ID 116 217 AF-like regionof CCACAATATATCCTGCCACCCC SEQ ID 116 218 AF-like region ofCCTGCCACCCAAGGAGCGACGCCTTCTGGCC SEQ ID 116

1. A cassette, comprising (1) a first polynucleotide, comprising asequence that is (i) nicked when exposed to an enzyme involved inbacterial-mediated plant transformation and (ii) not identical to abacterial border sequence; (2) a second polynucleotide, which may be (i)an imperfect or perfect repeat of the first polynucleotide, or (ii) abacterial T-DNA border; (3) a desired polynucleotide positioned betweenthe first and second polynucleotides; and (4) at least one of (a) UIregion, (b) DI region, (c) UF region, or (d) AF region.
 2. The cassetteof claim 1, wherein the first polynucleotide comprises a sequence thatis native to a plant genome.
 3. The cassette of claim 1, wherein thefirst polynucleotide is targeted and nicked by a vir gene-encodedprotein.
 4. The cassette of claim 1, wherein the first polynucleotideconforms to the consensus sequence depicted in SEQ ID NO:
 84. 5. Thecassette of claim 4, wherein the first polynucleotide comprises asequence that shares at least 70% sequence identity with the sequencedepicted in any one of the group consisting of SEQ ID NOs: 8, 9, 11-13,15-17, 28-37, 38-51, 85-86, 189, 190, 194-196, and
 198. 6. The cassetteof claim 1, wherein (1) the UI region comprises a sequence that sharesat least 70% sequence identity with at least one of SEQ ID NOs: 21 and199-208; (2) the DI region element comprises a sequence that shares atleast 70% sequence identity with at least one of SEQ ID NOs: 22 and102-114; (3) the UF region element comprises a sequence that shares atleast 70% sequence identity with any one of SEQ ID NO: 184-186 and211-214; (4) the AF region element comprises a sequence that shares atleast 70% sequence identity with the sequence depicted in SEQ ID NO:187, 188, or 215-218.
 7. The cassette of claim 1, wherein the cassettecomprises a UI region positioned upstream from the first polynucleotidecleavage site and an AF region that is downstream from the secondpolynucleotide cleavage site.
 8. The cassette of claim 1, wherein atleast one of (1) the portion of the cassette that comprises the UI andDI regions comprises the sequence depicted in SEQ ID NO: 131 and (2) theportion of the cassette that comprises the UF and AF regions comprisesthe sequence depicted in SEQ ID NO:
 132. 9. The cassette of claim 1,wherein all of the DNA sequences delineated by the first and secondpolynucleotides are plant DNA.
 10. The cassette of claim 9, wherein theplant DNA is endogenous to (1) a monocotyledonous plant selected fromthe group consisting of wheat, turf grass, maize, rice, oat, wheat,barley, sorghum, orchid, iris, lily, onion, banana, sugarcane, and palm;or (2) a dicotyledonous plant selected from the group consisting ofpotato, tobacco, tomato, avocado, pepper, sugarbeet, broccoli, cassaya,sweet potato, cotton, poinsettia, legumes, alfalfa, soybean, pea, bean,cucumber, grape, brassica, carrot, strawberry, lettuce, oak, maple,walnut, rose, mint, squash, daisy, and cactus, cucumber, melon, canola,apple, or pine.
 11. The cassette of claim 1, further comprising at leastone of (1) an overdrive element, comprising a sequence that is at least70% identical in sequence to SEQ ID NO: 88; (2) a pyrimidine-richelement, comprising a sequence that shares at least 70% sequenceidentity with at least part of any one of the sequences of SEQ ID NOs:21 or 199-208; (3) a sequence shares at least 70% sequence identity withat least part of any one of the sequences shown in SEQ ID NOs: 22 and102-106; (4) an AT-rich element, comprising a sequence that shares atleast 70% sequence identity with at least part of any one of thesequences in SEQ ID NO: 184-186 and 211-214; and (5) one or morecytosine clusters that comprise a sequence depicted in any one of SEQ IDNOs: 187-188 and 215-218.
 12. A plant transformation cassette,comprising at least one of (1) a polynucleotide comprising a sequencedepicted in any one of the group consisting of SEQ ID NOs: 8, 9, 11-13,15-17, 28-50, 85, and 86, wherein the DNA sequence comprising the 3′-endof the polynucleotide and DNA downstream thereof comprises the sequenceof SEQ ID NO: 122; (2) a polynucleotide comprising (i) a sequencedepicted in any one of the group consisting of SEQ ID NOs: 8, 9, 11-13,15-17, 28-37, 38-51, 85-86, 189, 190, 194-196, and 198, and (ii) a DNAsequence positioned downstream of the sequence of (i), wherein thesequences of (i) and (ii) together comprise a cytosine cluster thatcomprises a sequence that shares at least 70% sequence identity with anyone of SEQ ID NOs: 187-188 and 215-218; and (3) a polynucleotidecomprising a sequence depicted in any one of the group consisting of SEQID NOs: 8, 9, 11-13, 15-17, 28-37, 38-51, 85-86, 189, 190, 194-196, and198, wherein the 5′-end of the polynucleotide abuts a pyrimidine-richelement that shares at least 70% sequence identity with any one of SEQID NOs: 21 and 199-208.
 13. A method for transforming a plant cell,comprising introducing said cassette of claim 1 into a plant cell. 14.The method of claim 13, wherein the plant cell is located in either (1)a monocotyledonous plant or explant thereof selected from the groupconsisting of wheat, turf grass, maize, rice, oat, wheat, barley,sorghum, orchid, iris, lily, onion, banana, sugarcane, and palm; or (2)a dicotyledonous plant or explant thereof selected from the groupconsisting of potato, tobacco, tomato, avocado, pepper, sugarbeet,broccoli, cassaya, sweet potato, cotton, poinsettia, legumes, alfalfa,soybean, pea, bean, cucumber, grape, brassica, carrot, strawberry,lettuce, oak, maple, walnut, rose, mint, squash, daisy, and cactus. 15.The method of claim 13, wherein the first polynucleotide comprises asequence that shares at least 70% sequence identity with the sequence ofany one of (1) SEQ ID NO: 28-30 and wherein the plant cell is a tomatoplant cell; (2) SEQ ID NO: 32 and wherein the plant cell is an alfalfaplant cell; (3) SEQ ID NO: 33 and wherein the plant cell is a barleyplant cell; (4) SEQ ID NOs: 34-36 and wherein the plant cell is a riceplant cell; (5) SEQ ID NO: 37 and wherein the plant cell is a wheatplant cell; (6) SEQ ID NOs: 195-196 and wherein the plant cell is asoybean plant cell; (7) SEQ ID NOs: 51 and 194 and wherein the plantcell is a maize plant cell; (8) SEQ ID NO: 189, 190, and 198 and whereinthe plant cell is a Brassica plant cell.
 16. A cassette, comprising (1)a first polynucleotide, comprising a sequence that is nicked whenexposed to an enzyme involved in bacterium-mediated planttransformation; (2) a second polynucleotide that has greater than 70%sequence identity to at least 15 nucleotides of any one of SEQ ID NOs:133-137 or a functional homolog or derivative thereof; and (3) a desiredpolynucleotide positioned between the first and second polynucleotides.17. The cassette of claim 16, wherein the first polynucleotide is notidentical in sequence to a bacterial T-DNA right border sequence andcomprises the sequence depicted in any one of SEQ ID NOs: 8, 9, 11-13,15-17, 28-37, 38-51, 85-86, 189, 190, 194-196, and
 198. 18. A method fortransforming a plant, comprising (1) transforming a plant with atransformation plasmid that is suitable for bacterium-mediated planttransformation, wherein the plasmid comprises a transfer-DNA that isdelineated by (i) left and right transfer-DNA border sequences, andwhich comprises (ii) a non-autonomous transposable element, whichcomprises a desired polynucleotide, and a (iii) a transposase gene,wherein the non-autonomous transposable element and the transposase geneare positioned between the left and right border sequences, and (2)selecting a plant that stably comprises in its genome the non-autonomoustransposable element but not the transfer-DNA.
 19. The method of claim18, wherein at least one of the border sequences comprises a sequencethat is (i) nicked when exposed to an enzyme involved inbacterial-mediated plant transformation and (ii) not identical to abacterial border sequence.
 20. The method of claim 19, wherein thesequence of at least one of the border sequences comprises the sequencedepicted in any one of SEQ ID NOs: 8, 9, 11-13, 15-17, 28-37, 38-51,85-86, 189, 190, 194-196, and
 198. 21. The method of claim 18, whereinthe step of selecting a plant comprises positively selecting for a plantthat comprises the non-autonomous transposable element andcounter-selecting against a plant that comprises the transfer-DNA. 22.The method of claim 18, wherein the non-autonomous transposable elementcomprises the terminal ends of any one of an Ac, Spm, or Mu transposableelement.
 23. The method of claim 22, wherein one terminal end of the Acelement comprises the sequence depicted in SEQ ID NO: 139 and whereinthe other terminal end of the Ac element comprises the sequence depictedin SEQ ID NO:
 140. 24. The method of claim 18, wherein the plasmid ismaintained in a bacterium strain selected from the group consisting ofAgrobacterium tumefaciens, Rhizobium trifolii, Rhizobium leguminosarum,Phyllobacterium myrsinacearum, SinoRhizobium meliloti, and MesoRhizobiumloti.
 25. A method for transforming a plant with a desiredpolynucleotide, comprising infecting a plant with the bacterium strainof claim
 24. 26. A plant transformation plasmid, comprising a cassette,which comprises (1) a first polynucleotide, comprising a sequence thatis (i) nicked when exposed to an enzyme involved in bacterium-mediatedplant transformation and (ii) not identical to a bacterial bordersequence; (2) a second polynucleotide, which may be (i) an imperfect orperfect repeat of the first polynucleotide, or (ii) a bacterial T-DNAborder; and (3) a region comprising a virC2 gene.
 27. The cassette ofclaim 26, wherein the region that comprises the virC2 gene, comprisesthe sequence depicted in SEQ ID NO:
 167. 28. A method for transforming aplant with a desired polynucleotide, comprising infecting the plant witha bacterium strain comprising the plasmid of claim 26, wherein thebacterium strain selected from the group consisting of Agrobacteriumtumefaciens, Rhizobium trifolii, Rhizobium leguminosarum,Phyllobacterium myrsinacearum, SinoRhizobium meliloti, and MesoRhizobiumloti.
 29. A method for identifying a polynucleotide sequence that isinvolved in bacterium-mediated plant transformation, comprising: (i)isolating a candidate sequence from a source of genetic material; (ii)operably replacing one of (a) the first or second polynucleotide, (b)the UI region, (c) the DI region, (d) the UF region, or (e) the AFregion of the cassette of claim 1, with the candidate sequence; (iii)infecting a plant with the cassette using bacterium-mediatedtransformation; and (iv) determining whether the plant is stablytransformed with the desired polynucleotide, wherein a plant that istransformed with the desired polynucleotide indicates that the candidatesequence is involved in bacterium-mediated plant transformation.